MedWorm provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest medical blog items that have been tagged with 'bioit'. Sat, 03 Sep 2011 02:48:40 +0100 http://www.medworm.com/index.php?rid=4653491&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FX92wTUvET3w%2F Tweet The scale of modern life science research, where scale is not just about data volume, but also about rate of change, number of users, geographic scale, etc means that resources have to look at how they provide services differently and, more importantly, funding agencies and philanthropists have to decide where to draw the line. Is this an opportunity for commercial efforts? Is the market ready to do this, or are they willing to live with overall inefficiencies and limitations? Is there a tiered model that would be acceptable. Recent discussions and observations of what various companies and orgs are doing leads me to believe that we need to really think hard about overall efficiencies and consider the value of time. More later (Source: business|bytes|genes|molecules) business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=4653491 Tue, 29 Mar 2011 07:03:03 +0100 4653491 http://www.medworm.com/index.php?rid=4389299&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FpXVd9W04oME%2F Tweet Last night I was attended a rather interesting private event. I won’t talk about the event in detail since it was private, but it was a mix of life science folks and technologists, with the latter pushing the former to try and get a sense of scale and boundaries. The difference in mindset between engineers and scientists was so apparent at that time. While much of the discussion was centered around really hard biological and computational problems I was reminded that science is not just about solving really hard problems. Much of it is incremental, a result of access to new types of experiments and data and increased knowledge in the field. These days, one of the core challenges to this incremental form of discovery is that a number people are bound by storage, by computation... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=4389299 Sun, 23 Jan 2011 06:01:55 +0100 4389299 http://www.medworm.com/index.php?rid=4207448&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FJeaBTmDAQKQ%2F Tweet One of the most frustrating aspects about computational biology and chemistry for me used to be the lack of a hacker culture. Never is that more apparent to me than when I am listening to podcasts like The Changelog or Ruby 5. However, I am upbeat about that changing, despite the odds. There is a good subculture of people in the life sciences who care about good software, building good “products”, even if they are used only internally. Among the circles I hang around in, there is interest in bursty work, APIs, open source libraries, sharing best practices and building a community of programmers and developers, regardless of subfield. I look forward to the day that we have a thriving community of data scientists, software engineers, and systems engineers all coming toget... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=4207448 Sun, 28 Nov 2010 03:14:59 +0100 4207448 http://www.medworm.com/index.php?rid=3845239&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FShGFWOdSkgM%2F Image of Matt Wood I’ve had the luxury of working in some very interesting areas; large scale protein structure prediction, physics-based approaches to drug discovery, data management for all kinds of molecular profiling data, and high-scale distributed infrastructure. I also have had the fortune of meeting some of the brightest people in the world at their craft over the years. In particular, over the past couple of years, I’ve met or observed some exceptionally bright people at the forefront of information retrieval and data mining. While there is a lot of naive, follow the latest trend, activity, there is also a lot of excitement. The web produces a lot of data, and many smart folks are trying to make sense of all that data. I am obviously biased, and can never really sto... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3845239 Sun, 08 Aug 2010 18:29:47 +0100 3845239 http://www.medworm.com/index.php?rid=3573866&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FB5SkvTRKfu0%2F One of the best posts ever on data management in the sciences comes to us via Titus Brown. The data management plan he proposes is one that is battle tested in many laboratories across the world. Neil captures the actionable items from the above blog post I am still laughing. I should be crying. Related articles by Zemanta Summer Course: Analyzing Next-Generation Sequencing Data (softwarecarpentry.wordpress.com) BEACON Funded! (softwarecarpentry.wordpress.com) (Source: business|bytes|genes|molecules) business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3573866 Tue, 18 May 2010 04:18:58 +0100 3573866 http://www.medworm.com/index.php?rid=3556282&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FOX2IN5IiNdM%2F I recently wondered if there would be a time that scientific data APIs would get the kind of developer excitement that the Twitter API gets. To some extent that is wishful thinking. After all the type of data you get via Twitter and the type of data you get from next-gen sequencing are quite different and require a different level of expertise and understanding. But I do believe that smart developers especially those with a data mining bent can learn enough biology to really help and extend the field. I’ve been in enough meetings recently where there has been quite a bit if contention of roles in the life sciences. Some of it is semantics, but a lot of it is real. We have algorithm developers, bioinformaticians, biologists, software developers and perhaps roles that I am forgetting,... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3556282 Tue, 11 May 2010 22:33:50 +0100 3556282 http://www.medworm.com/index.php?rid=3363772&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2F2zc50UROtzQ%2F Dan Koboldt has a great post on the state of sequencing in 2010 (can we drop “next-gen” now?), and beyond I guess. It’s certainly getting crowded out there, and it did look like that the major players were essentially fighting for the same space and share of the market, but based on what Dan says, that seems to be changing. I should add that I am not in the trenches, and my interests lie on the data management, analysis and infrastructure side of things, so can’t comment on individual technologies per se. It’s interesting to see how various players seem to be positioning themselves, although where folks end up and who survives will depend on all kinds of factors. The scientific market is fickle and quite honestly, the factors that define success are not alway... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3363772 Sat, 13 Mar 2010 21:19:29 +0100 3363772 http://www.medworm.com/index.php?rid=3089478&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FaqUjQTO3o9Q%2F It is time for a whole new approach. Front-line biology cannot function without these resources, so solutions must be found at both national and international levels. That’s from an editorial in Nature talking about the need to change the way data resources are funded, a topic I have visited before. In this particular case, the resource under question is The Arabidopsis Information Resource (TAIR), which had been funded by the NSF for a decade but is seeing that sole source of funding phased out. As the editorial points out, such challenges are not unique to TAIR, but a problem facing biological databases and repositories, i.e. part of the core infrastructure for the life sciences. I say that because to sustain any data resource you need to sustain infrastructure as well as the devel... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3089478 Tue, 15 Dec 2009 05:48:09 +0100 3089478 http://www.medworm.com/index.php?rid=3075709&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2F4w3p-VKmQbg%2F Image by dullhunk via Flickr In a great blog post at Code for Life, Grant Jacobs writes By contrast, early bioinformatics work was almost invariably founded on biological concepts from the onset. A biological issue was raised and then a technique to address that issue was presented. That is, theoretical biology was the foundation on which [early] bioinformatics was built. I fear this is being lost in the mass-data and technology-hype driven bioinformatics. It seems to me that unless companies and research groups are careful many will waste time and money “stamp collecting and cataloging”. Certainly the organized data is useful, but only if it is applied with biological principles Grant writes this in the context of the early days of bioinformatics, a time when there was a lot of the... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3075709 Thu, 10 Dec 2009 03:43:17 +0100 3075709 http://www.medworm.com/index.php?rid=2809848&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FruD3vCSXd08%2F Over the next few months, I’ll be giving a bunch of talks about large scale data. I will be talking at Hadoop World about “Hadoop for Bioinformatics“, at a Cloud Computing for Hedge Funds and at Supercomputing. Thinking through what I want to cover at all these talks has my brain in overdrive these days. At the same time discussions with various people facing data-related challenged provides a reality check and reminds me that there is still a long way to go. The one concept that people need to start putting their head around is the relative location of compute and data. Many people still think along the “move data to the compute” paradigm. When our data sets were small, this was not a problem. As instruments provide more and more data, ever faster, that tends... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=2809848 Sat, 19 Sep 2009 03:33:17 +0100 2809848 http://www.medworm.com/index.php?rid=2796486&cid=t_104570_107_f&fid=36698&url=http%3A%2F%2Fminingdrugs.blogspot.com%2F2009%2F09%2Finnovation-20-looking-for-strategy-in.html "You can’t control what you can't measure." [Tom DeMarco]I am strongly believing in people-centric innovation for drug design and health care. Still, we have serious challenges to solve before this can happen, and a lot of them are in-vivo, not in-silico:Get rid of the negative group dynamics.Accept information overload and embrace collaboration.Bridge silos, e.g. chemical data silos, but also break-down legal or license hurdles, e.g. by using micropayments.Please find below the slides and handout for my talk in October on the BioIT World conference. The conference will cover a large range of life science topics, e.g. -omics, semantics, technology, bioinformatics, life science software, collaboration platform, etc. This is all very exciting and I am looking forward to those talks and mee... Mining Drug Space blogs http://www.medworm.com/rss/comments.php?id=2796486 Mon, 14 Sep 2009 18:21:00 +0100 2796486 http://www.medworm.com/index.php?rid=2712294&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2Fqm-xYwthDJk%2F Over the years, I’ve written about the web as a connected entity, with nodes notifying other nodes of an event or action. At various times this has been called the “just in time” web and more recently, in a narrower context, the distributed self. However, it is only in the last several months that I have come to appreciate the inefficiencies of polling and the potential of an event-based, notifications oriented web architecture, and I do believe as we stream more and more scientific data, such architectures are only going to get more common in the sciences, or at least I hope they do. In a recent blog post about Smart Clients, Ilya Grigorik writes As more and more browsers start adopting HTML 5 features I’m hoping to see WebSockets become a reality within the next ... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=2712294 Wed, 19 Aug 2009 07:33:46 +0100 2712294 http://www.medworm.com/index.php?rid=2630315&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FhFJFPSuH1HQ%2F Been thinking a lot about data, not in the least cause I have to start thinking about my talk at Supercomputing. There have also been a number of recent meetings, podcasts, blog posts, etc that have me thinking about data, and managing data again. I won’t talk about the specifics from the meetings I’ve been in, but a lot of the discussion and thinking has been around large quantities of data, ranging from unstructured data to highly structured data and how we can analyze them more efficiently. The one thing I can talk about is this blog post describing the release of HadoopDB. HadoopDB is a new stack that combines PostgreSQL, Hadoop and Hive, essentially combining MapReduce with DBMS technologies, specifically targeted at the analytics crowd. I won’t talk about pluses and... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=2630315 Thu, 23 Jul 2009 06:28:10 +0100 2630315 http://www.medworm.com/index.php?rid=2512434&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FJum_7KEqAsY%2F Image via Wikipedia So the latest Top 500 list is out, so why doesn’t it excite me as much as it used to. Well partly cause many of those machines are not easily accessible, while other computing resources are within reach. Perhaps partly because for a lot of the work I am interested in doing, you don’t really need a machine in the top 500. Of course, having access to a machine there allows you to address some problems you couldn’t any other way, and IMO they should only be used for such problems. One of the better posts about this years list comes from Chris Peters at Intel. He presents a different perspective on the list and notes some trends. For example, the 10th fasted machine on this years list drives more FLOPS than all 500 machines on the 2000 list. While the... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=2512434 Thu, 25 Jun 2009 06:09:08 +0100 2512434 http://www.medworm.com/index.php?rid=2512437&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2F9FxigN-boEI%2F In a blog post last year James Hamilton wrote about workloads in large scale network file systems. In his summary about of study on the subject he writes Some of the important points that spring out for me: the percentage of random access is increasing; for those accesses that are sequential, the runs are longer; file sizes are increasing, data is getting colder; file lifetimes are increasing; and client usage has very high skew. Those patterns sound a lot like some of the patterns I have seen in the life sciences recently, especially as we have to handle increasingly larger data volumes, which have varying levels of access patterns and usage. Seeing some of the data challenges that people close to home have been seeing, esp significantly higher write to read ratios, which makes caching... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=2512437 Sun, 14 Jun 2009 06:14:55 +0100 2512437 http://www.medworm.com/index.php?rid=2473897&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FajvsnJzwVfI%2F I have been invited to give a Masterworks talk on Data Challenges in Genomics for Supercomputing 09. I would like to dive into the details about the technical and scientific challenges of high throughput genomics, from microarrays to next gen sequencing and beyond and how we need to be manage these data more efficiently. While part of my talk will be about my day job, I want it to be informed by challenges we face today and will face tomorrow as a scientific community. So to try and capture many of these challenges and gather facts and information I have started a wiki page which I have made public. Please feel free to add to that page with ideas and topics that interest you. To do so, you will have to login as user sc09 and password computing. I request that you add your name to any major... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=2473897 Sun, 14 Jun 2009 04:51:36 +0100 2473897 http://www.medworm.com/index.php?rid=2469825&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FQaTDdTcj_UQ%2F I’ve written about software failures in the past. As I get a better understanding of scale and architectures and talk to others about some of the core design principles of systems at scale, e.g. Recover Oriented Computing (also see this talk by James Hamilton), I realize how little most of us in the life science world think about some of these design principles. Most people in this space do not run data centers, and usually have limited access to resources at massive scale. Yet, we are going towards a data intensive world, and a world in which we could, in princple, perform massive optimization problems. So the question to ask is, when will we start seeing some of these design patterns start becoming the norm rather than the expception for computing in the life sciences? When will we... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=2469825 Wed, 10 Jun 2009 07:06:01 +0100 2469825 http://www.medworm.com/index.php?rid=2442320&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FMdHk3k0ZA8s%2F I recently heard someone talk about software as being operational. The context was large scale systems and how it is important not just to run hardware systems that operate at scale but also software that operates at scale. And having spent a lot of time lately in a world where operational excellence is paramount as well as the Hadoop world, the importance of operational software is becoming only more evident. As we work with very large data sets that need to be processed across 100’s, even 1000’s of commodity compute nodes, you need to run software that accepts and embraces failure. What makes the Hadoop framework work isn’t just the part that you can run map-reduce jobs, but the part where data is replicated in multiple locations, where the filesystem is distributed acr... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=2442320 Mon, 25 May 2009 07:02:01 +0100 2442320 http://www.medworm.com/index.php?rid=2349284&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FGS_LscZ1E5A%2F Image via Wikipedia As readers of bbgm know, one of the subjects that interests me the most is computing, even though I am hardly a guru, but I’ve been around long enough and close enough to the world of computing to notice and observe various trends in this space. Perhaps the most recent trend, and it appears a new phrase in the computing lexicon is data intensive computing, something that life scientists should be very cognizant of today, as I talk about in Science Big, Science Connected. This interest in data intensive computing and recent exposure to data centers and large scale operations has led me to pay even more attention to some blogs I’ve been following for a while. Specifically, two blogs that I read religiously are those of James Hamilton and Dan Reed. James write... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=2349284 Mon, 13 Apr 2009 04:49:27 +0100 2349284 http://www.medworm.com/index.php?rid=2323813&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FJnXhyOQpwqg%2F Image via Wikipedia Every all-hands meeting I learn something new. This time the word that I heard Jeff Bezos use was trystorming, described as brainstorming, except that instead of talking about things you actually try things out. That’s something that most of us can relate to. Many of us spend too much time doing to former, although recent trends in iterative software development, availability of cheap on-demand computing, and the rise of frameworks like Ruby on Rails and SCMs’ like git which encourage rapid prototyping are definitely a positive trend, at least in the software space. Also this week, I got my hands on a paper by Sanjoy Ray Director of Technology Innovation at Merck written for Pharma Focus Asia. Unfortunately you need to register to get to the paper (free I be... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=2323813 Sun, 05 Apr 2009 02:22:47 +0100 2323813 http://www.medworm.com/index.php?rid=2232810&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FHtt9qwBjCck%2F Image via Wikipedia Pierre asks How !#@$* do you manage 1000 genomes ??!. Perhaps we should be asking how we are going to manage 10,000 genomes, or 100,1000 and all the variants, and links between genotype and phenotype. This is going to get harder before it gets easier, and moving that data around will become very very difficult. (Source: business|bytes|genes|molecules) business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=2232810 Mon, 02 Mar 2009 04:29:47 +0100 2232810 http://www.medworm.com/index.php?rid=2232812&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2Fmwp4zq9WeMw%2F Image by Getty Images via Daylife While on the subject of open and pharma, a bioinform article (sub reqd) tells us about Unison, a protein sequence analysis platform from Genentech that has been released under the Academic Free License (why not the Apache License since they are very similar). What is Unison? Unison is a compendium of protein sequences and extensive precomputed predictions. Integration of these and other data within Unison enables holistic mining of sequences based on protein features, analysis of individual and sets of sequences, and refinement of hypotheses regarding the composition of protein families Essentially Unison is a data warehouse, which includes a number of protein sequences, and a bunch of pre-computed data. They have also released the complete schema, AP... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=2232812 Sat, 28 Feb 2009 06:14:08 +0100 2232812 http://www.medworm.com/index.php?rid=2131355&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2Fen1m-Gd6w5A%2F Image via WikipediaShahid Shah had a post about TrialX the other day, which made me a little curious about the site and its goals. The TrialX tagline is Enabling patients to find new treatments (and clinical trials). Their mission is to To help save lives by providing patients access to new treatments in an easy and timely manner. So what does all that mean? TrialX is a HealthIT startup, whose core technology matches participants to clinical trials (as an aside, why do sites have to add words like “groundbreaking” and “first of its kind” to About pages?). Essentially the goal is to create a platform for patients to find trials of interest and for investigators to find patients for trial recruitment. So underneath the hood you have a search engine, a matching algorit... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=2131355 Sat, 24 Jan 2009 19:22:25 +0100 2131355 http://www.medworm.com/index.php?rid=2121804&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FNRHoilOsbeE%2F Image via WikipediaTechnology Review has an article about visualization software specifically designed for big data. In recent years we have seen trends towards algorithms and methods designed towards dealing with large amounts of data using commodity hardware. We’ve already seen the Map-Reduce algorithm being applied to any number of data driven problems, including the analysis of large molecular dynamics trajectories. The software described in Technology Review, likely best described in Attila Gyulassy’s PhD Thesis, takes the common approach of breaking down a problem in smaller chunks, easier said than done when dealing with visualization. Now, I am not exactly a visualization guru, so how good this work is in practice I cannot say. But it is part of a trend that I really l... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=2121804 Thu, 22 Jan 2009 05:32:21 +0100 2121804 http://www.medworm.com/index.php?rid=2021565&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2F0cOtEK4BTa0%2F For the longest time, I’ve hoped that the tech world would see the beauty of science, and the complexity of modern biology. A lot of the material that makes it into tech blogs is futuristic, alarmist, or plain old misinformed, or at the very least misrepresented. Well all that changes today. Matt Wood, someone whose thoughts on big data have influenced my own quite a bit, is now blogging for the O’Reilly Radar. You have someone from the trenches of modern high throughput biology writing for one of the better tech blogs. This can only be good. Matt’s first post is about the Challenges for the new genomics. His talk on The New Genomics is worth a listen as well (Source: business|bytes|genes|molecules) business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=2021565 Tue, 09 Dec 2008 05:57:58 +0100 2021565 http://www.medworm.com/index.php?rid=2017621&cid=t_104570_132_f&fid=35014&url=http%3A%2F%2Fharijay.wordpress.com%2F2008%2F12%2F05%2Fa-naive-biochemist-wakes-up-to-the-closed-world-of-chemical-abstracts-and-such%2F We have a project in the lab that involves screening small molecule inhibitors that inhibit the transport activity of a membrane protein on a “lab scale”  . Having identified one such inhibitor we intended to look for similar molecules that share the same substructure . Substructure query is a standard procedure in chemical informatics . In the past I have screencast the use of the Sigma-Aldrich service to identify molecules from sigmas catalog based on similarity .  However  considering the wealth of biochemically relevant  information PUBCHEM offers , I was curious to try out the substructure query at PUBCHEM .  This Pubchem service works great and is very feature rich ( screencast coming soon) and gave me several molecules which could be of interest in my screen. T... The Omics world blogs http://www.medworm.com/rss/comments.php?id=2017621 Fri, 05 Dec 2008 16:18:55 +0100 2017621 http://www.medworm.com/index.php?rid=2005828&cid=t_104570_132_f&fid=35014&url=http%3A%2F%2Fharijay.wordpress.com%2F2008%2F12%2F02%2Fof-bubbles-and-funding%2F I am writing to attempt to describe my opinions after reading a very insightful commentary written by Gregory Petsko in the September issue of Genome Biology ( doi 10.1186/gb-2008-9-9-110) titled “When Bubbles Burst” . In that article Greg Petsko analyses the parallels between the current Economics bubble and the Big-science bubble ( my words). Just as we can attribute the financial bubble to the un-regulated growth of the financial industry , we can possibly attribute the many problems ailing the research establishment to the un-regulated growth of the “omics” bubble. We all have witnessed the move of all Science into the genomic age. We have witnessed the gradual shift of federal research Dollars to consortium based science. Whether it is the cancer genome or stru... The Omics world blogs http://www.medworm.com/rss/comments.php?id=2005828 Tue, 02 Dec 2008 16:58:44 +0100 2005828 http://www.medworm.com/index.php?rid=1933315&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FGj0d_xsp6EY%2F Image via WikipediaI am not a lawyer, and while I have some opinions and some knowledge of FDA guidelines, I want to use the current pharma story du jour to highlight something that we need to do. I am sure anyone who listened to NPR today heard about Wyeth’s anti-nausea drug, Phenergan. To cut a long story short, the drug was administered to Diana Levine, a musician from Vermont, via the IV-push method, which has a small risk of inducing gangrene (if pushed into the artery). At issue, whether Wyeth should have changed the label having known about the issue. I won’t go into what Wyeth should have done, or not. That case is now before the US Supreme Court. I want to talk about the importance of pharmacovigilance, about the need to essentially never end clinical trials. We often ... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1933315 Tue, 04 Nov 2008 05:22:15 +0100 1933315 http://www.medworm.com/index.php?rid=1750234&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FzXOTlT2fFBY%2F What are the things that evolution has at its disposal to define a creature, to mix and match the parts, and eventually come up with a unique organism that’s going to live its life and try to reproduce? – Will Wright, gaming innovator Every time I take a “how big a geek are you” test, I fail, since I am not a gamer. That’s by choice. If I ever start, I am doomed. There is not enough time for all the things I care about as it stands, especially music, so gaming has always been kept at arms length. That said, cool games, and ideas in games are always of interest. Spore, which gets released on Sunday, has to be among the most highly anticipated, most hyped games since, well I suppose, GTA IV. Well, when you bring a cool game and genetics together, you get my attenti... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1750234 Tue, 02 Sep 2008 06:20:50 +0100 1750234 http://www.medworm.com/index.php?rid=1734055&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FHPHWvx0E8_Q%2F Image via Wikipedia One of the talks I wanted to attend at OSCON, but missed in the blur of booth duty and conflicting sessions was Aaron Thul’s talk on Electronic Medical Office Logistics (EMOL). The talk was a talk on PostgreSQL talk, but wrapped around what it takes to develop an EMOL solution. The good news is that a lot of the OSCON talks are available online. Check out the pdf for Aaron’s talk, or follow on for some comments (based on just the slides) or do both. The talk essentially goes through how a FLOSS stack (with one notable exception) can be used to build a system that can collect data from EMRs and other data sources, while maintaining regulatory standards and providing a degree of automation. I remember the first time I was sitting in on a talk on EMRs some year... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1734055 Tue, 26 Aug 2008 03:47:22 +0100 1734055 http://www.medworm.com/index.php?rid=1634968&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F338671378%2F Image via WikipediaThe virtual laboratory, the stuff of dreams and increasingly reality. We’ve talked about CARMEN and similar projects in the past, efforts that enable collaboration and provide users with the a platform to deploy algorithms and services. We’ve also talked about NanoHub in the past. A press release on entitled Virtual world is sign of future for scientists, engineers reminded me that I had not visited the site for a while It is definitely one of the better designed sites of its kind out there, and looking at the site again and reading the press release got me thinking to a couple of themes that are no strangers to these pages (1) Is there a role for microcommunities in science? (2) Is the future of software delivery in science a virtual one? Lets talk about mi... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1634968 Fri, 18 Jul 2008 04:27:26 +0100 1634968 http://www.medworm.com/index.php?rid=1582978&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F328170314%2F Image via WikipediaOne of the thoughts I’ve always had over the years in life science software was the need to adjust to constantly changing needs and technologies. In the world of “omics” software, where the technologies generating the data, as well as the data types keep evolving, it gets pretty darn complicated to build solid software projects. So, a paper on Systems biology driven software design for the research enterprise naturally caught my interest. The paper, from John Boyle et al discusses the informatics infrastructure being developed at the Institute for Systems Biology. What struck me as I was going through the first part was that there was no mention of RESTful architectures, at least explicitly, which was somewhat of a disappointment. The architecture they ... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1582978 Sun, 06 Jul 2008 17:05:07 +0100 1582978 http://www.medworm.com/index.php?rid=1535811&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F316345476%2F Image via WikipediaGreat post by Sandra Porter on GenBank as an information resources. Over the years the NCBIs database resources have mushroomed, but continue to be generally regarded as the primary resources for genes and gene-related information (along with the EBIs resources). I’m going to focus on one question. Centralization and data quality. In general, to deposit something in a central repository, you should have the following criteria A minimal set of criteria that need to be met prior to deposition A robust version control system, which allows you to trace back to changes and allows scientists to compare their results across changing genomic information APIs that are used both internally and externally, that provide consistent programmatic access to the underlying data mo... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1535811 Fri, 20 Jun 2008 17:20:34 +0100 1535811 http://www.medworm.com/index.php?rid=1508517&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F309874956%2F One of my favorite technologies is XMPP, the technology underlying many IM clients/services including Jabber and GTalk. It’s also one of the nicer features that Twitter supports (when it’s working). Recently, Marshall Kirkpatrick wrote a nice post about XMPP in the context of Google Finance. The part that caught my attention immediately was the part about Engine Yard will use XMPP for it’s forthcoming Vertebra cloud computing service. The role of XMPP will be to communicate between all the applications in the cloud, essentially as a messaging framework. Essentially they will have a bunch of agents running on every slice/node on the cloud and essentially announcing when a slice comes online/offline and a workflow engine that coordinates multiple agents. Now lets move to a... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1508517 Wed, 11 Jun 2008 20:15:36 +0100 1508517 http://www.medworm.com/index.php?rid=1454483&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F294320652%2F Eli Lilly is opening up. According to an article in Bio-IT World, Eli Lilly has open sourced its Discovery IT platform. Anyone who has been around pharma probably did a double take, but after listening to John Reynders at the Bio-IT World Conference, I am not as surprised (apparently this effort started while he was at Lilly). The underlying question, as framed by Susie Stephens, principal research scientist with Lilly. Do we [biopharma] all really need to manage very similar resources or are there areas where we can work together? Is this the sign of a new outlook at pharma. Perhaps only just a little bit, but there are clear signs of a change. Consortia sharing pre-competitive information, companies making GWAS data public and Lilly’s efforts here. I think it is clear that peopl... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1454483 Tue, 20 May 2008 14:56:54 +0100 1454483 http://www.medworm.com/index.php?rid=1418465&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F282807163%2F This weeks Bio-IT World meeting was all about data storage. Driven by the needs of integrating complex, heterogenous data and most of all by next gen sequencing, it’s amazing how much data the life sciences are generating and how poorly prepared we are. I won’t necessarily mention names, but there are places which have data hitting the petabytes AFTER throwing away most of it. How do you access this data? How do you back it up? What kind of data centers do you need? What kind of power do you need? When people are worried about the city being able to handle their power needs then there is cause for concern. It is also why I think the future of scientific data generation needs to be thought about like Google, etc view data, infrastructure and data access. What if we had a Big Tab... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1418465 Sat, 03 May 2008 16:00:39 +0100 1418465 http://www.medworm.com/index.php?rid=1409769&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F280709573%2F A quick report on Day 2 of Bio-IT World. The day started with a keynote by Josh Boger, founder and CEO of Vertex. His talk spanned several real world examples and some food for thought. Highlights Vertex has made active use of a MedChem ELN, which has been extended to their entire MedChem community, including external partners. In his own words the goal was “enabling the virtual research organization” Metric of success was user adoption and there were some good analytics supporting uptake He spoke at length about the HCV program, where they have used extensive predictive modeling and simulation Clinical data has backed up their predictive modeling (they’re in Phase III now) They have avoided some experiments (carried out by competitors in one case) that their models sug... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1409769 Wed, 30 Apr 2008 10:43:39 +0100 1409769 http://www.medworm.com/index.php?rid=1407046&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F280023869%2F Detailed blog posts will follow when I have some additional cycles, but thought I’d share some quick thoughts on day 1 of Bio-IT World. My conference started with a workshop on data visualization, which was mostly about the importance of visualization for making sense of multidimensional data sets and what kind of visualizations could be done. My take aways from the talks There was a distinction made between statistical methods and data mining and presenting information to humans. Life science data is inherently multiscalar and reducing dimensions without losing information or creating artifacts is not trivial Importance to create systems that can help scientists go through a workflow and predict visualizations, and help guide the user to the most appropriate visualization for the r... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1407046 Tue, 29 Apr 2008 10:54:07 +0100 1407046 http://www.medworm.com/index.php?rid=1239292&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F237123988%2F Nathan Wolfe’s work on disease surveillance is fascinating. I wonder what kind of role informatics can play here. My brain is mashing up iPhones, stream querying, triple stores and maps Further reading Streambase: Query your streaming data The CDC embraces the Semantic Web Technorati Tags: Disease Surveillance, Infectionus Diseases, Nathan Wolfe (Source: business|bytes|genes|molecules) business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1239292 Mon, 18 Feb 2008 19:04:58 +0100 1239292 http://www.medworm.com/index.php?rid=1097689&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F201406094%2F As we build collective intelligence applications, which are the heart of Web 2.0, we need to make sure that their inner workings remain open and transparent, or we may fall into the same trap that ended up bedeviling Wall Street in this past year, in which no one understood any longer just how the machine they’d built was going to perform, and the Golem was out of control. The above quote comes from a post by Tim O’Reilly where he discusses politics and Warren Buffet. It struck me as telling that the peer review process and the academic model also forms an analogous “machine”. I am not an academic, so I could be wrong, but from what I read, hear, and from my memories as a graduate student, there appears to be a lack of transparency in many processes. What are the cr... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1097689 Mon, 17 Dec 2007 01:16:54 +0100 1097689 http://www.medworm.com/index.php?rid=1097690&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F201315504%2F In conclusion, one is left with a lot of questions. Just reading the two pieces, and even my own writings, and you can see that the industry is struggling as computing, even high performance computing, becomes increasingly commoditized, and user behavior evolves. How all the advances we’ve made in chip design and architecture will be put into practice is conjecture at this point. To some extent, if the cloud is where the action is, the user doesn’t really care. They just want their work done. My personal interest is to see the impact of the cloud and supercomputing on science. Historically, it’s tended to be difficult to get access to vast, scalable resources of compute power. Is that going to change? Will our software be up to the task? Science has done, by and large, a ... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1097690 Sun, 16 Dec 2007 20:23:55 +0100 1097690 http://www.medworm.com/index.php?rid=1088745&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F198949970%2F To beat your competitors, are you devoting more than 50% of your capital expenditures to information technology? If so, you’re not alone. Businesses worldwide pump $2 trillion a year into IT. But like many broadly adopted technologies—such as railways and electrical power—IT has become a commodity. Affordable and accessible to everyone, it no longer offers strategic value to anyone. – Nick Carr in IT Doesn’t Matter (Harvard Business Review, May 2003) Like Nick Carr (I’ve actually never read the book, just the paper), I believe that IT doesn’t matter, not on its own merit anyway. What does matter is how information is leveraged, and how it is distributed. In other words what matters is the implementation and acknowledgement of IT as a resource, one that can be... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1088745 Wed, 12 Dec 2007 02:18:09 +0100 1088745 http://www.medworm.com/index.php?rid=1080395&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F197010004%2F A recent Tweet from factoryjoe aka Chris Messina is worth putting up here. It just dawned on me that startups are obsolete. Sustainable, distributed bursty work is the future. The other day I blogged about the SourceForge Marketplace and a microeconomy developing around expert offerings. Chris takes the thought one step further. Is the future of web-based “startups” not a formal legal long running entity, but high value projects where you get together with a set of people, perhaps via a network of some sort (the “sustainable” is key in the above tweet)? I am not completely sure. However as work gets increasingly distributed, and resources go into the cloud, I can see the forming of small distributed teams or individuals that come together on a project by project b... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1080395 Sat, 08 Dec 2007 04:03:09 +0100 1080395 http://www.medworm.com/index.php?rid=1048511&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F189885411%2F Interesting post over at Web Worker Daily, of all places, on Visicu. To an extent they stretch the definition of web work in the context of eICU, bugat nevertheless it’s a look into the potential future of medicine. If you recall I wrote about a BT-funded report which emphasized telemdicine. The eICU is part of the pharma future envisionsed in that report. So what is the Visicy solution? The eICU® solution is sold to large, multi-hospital health systems that want to improve the quality of their intensive care unit (ICU) care. If you can understand how air traffic controllers and onboard technology for pilots keeps fliers safe, you’ll be able to understand how an eICU facility keeps patients safe. In other words, the idea is to create a system that allows to monitor patients rem... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1048511 Sat, 24 Nov 2007 18:02:36 +0100 1048511 http://www.medworm.com/index.php?rid=1002808&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F179813722%2F A post by Egon on Biospider got me thinking a little. There is a trend in the life science industry to look at scientific information in some of the same ways as enterprises have historically looked at business intelligence. A quick search for the term “business intelligence” will give you solutions from Microsoft, Oracle, SAS, etc. The goal of business intelligence is to help your make decisions faster and more efficiently. The data being collected by an enterprise are a valuable source of knowledge and using large data warehouses and complex analytics, companies have made a killing in this field. Via Lijit, I found this post by Joerg where he defines Business Intelligence. Now read that definition and think about the role of informatics in a drug development environment. If ... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1002808 Mon, 05 Nov 2007 01:32:46 +0100 1002808 http://www.medworm.com/index.php?rid=964607&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F172226054%2F The other day, at Web 2.0, Jeff Huber, Google’s VP of Engineering, said something that really resonated with me What we see is applications fundamentally changing. Just like the model for content changed from monolithic sites, now applications are going to be feeds and containers. A lot that you have heard here is about platforms and who is going to win. That is Paleolithic thinking. The Web has already won. The web is the Platform. So let’s go build the programmable Web. The internet as platform is going to become a recurring series here on bbgm, adding to the one on personalized medicine. There are two areas that I am fascinated by and “think” that I know something about. Anyway, lets start with a simple example of the web as platform in the life science space. Via ... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=964607 Fri, 19 Oct 2007 22:41:16 +0100 964607 http://www.medworm.com/index.php?rid=944611&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F168461585%2F If there are two people from the tech world whose blogs I would choose to read if I was given a choice of two, they might just be Jon Udell and Jeff Jonas, and they will forever be joined in my mind, cause I found Jeff via Jon. Unfortunately, I have never had a chance to meet Jon Udell, but I have had the chance to talk to Jeff. Previously I talked about the data path. I would like to extend the thought on persistent context a little further. I have long felt that one of the flaws in most software design is a lack of context. If I am in one view where certain actions are not possible, why do I need to know about 10 things that don’t make sense. Similarly with data, maintaining context is critical, since the data only make sense in the appropriate context. “Andy is naked” ... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=944611 Thu, 11 Oct 2007 14:06:12 +0100 944611 http://www.medworm.com/index.php?rid=932042&cid=t_104570_132_f&fid=35014&url=http%3A%2F%2Fharijay.wordpress.com%2F2007%2F10%2F06%2Fi-feel-chicken-gunya-can-social-networks-help-track-emerging-diseases%2F I remember being particularly amazed at Jonathan Harris and Seepandar Kamwars  “We feel fine”  visualization based on extracted statements from blog posts around the world. Reading about the re-emergence of dengue fever , chicken-gunya , west-nile and other viruses across South Asia, I started wondering if there are ways of keeping track of emerging pathogens using the many social networks that span the Globe. In many countries there is no paranoia associated with sharing health information like there exists in the developed world. Even if the paranoia exists like it does in the US. We are curiously caught in a world where people reading my blog are more likely to know I have contracted the flu than any two of my healthcare providers who need that information to treat me bett... The Omics world blogs http://www.medworm.com/rss/comments.php?id=932042 Sat, 06 Oct 2007 06:57:54 +0100 932042 http://www.medworm.com/index.php?rid=927877&cid=t_104570_132_f&fid=35014&url=http%3A%2F%2Fharijay.wordpress.com%2F2007%2F10%2F04%2Fof-6-web-hosts-and-dying-web-apps%2F Just yesterday I was reading tiagos blog where he requested hosting for a computational intensive bioinformatics web-app that he wrote. The application queries and sytematizes mitochondrial genome information from entrez databases, and I assume would be quite useful to animal geneticists and ecologists. Tiago is physically moving institutes and his blog posts talks of his fears of how the app might die if his personal computer goes down. In one of my personal projects , I have been wrestling with cloning kappa light chains from several monoclonal antibodies that I generated. The cloning required a good knowledge of the anitbody light and heavy chain leader sequences . Several papers I was reading reference the Kabat and Wu database, which catalogs the thousands of sequences of antibodies a... The Omics world blogs http://www.medworm.com/rss/comments.php?id=927877 Thu, 04 Oct 2007 16:37:38 +0100 927877 http://www.medworm.com/index.php?rid=925293&cid=t_104570_132_f&fid=35014&url=http%3A%2F%2Fharijay.wordpress.com%2F2007%2F10%2F03%2Frefseq-and-uniprotkb-groups-collaborate%2F A lot of you have heard me complain ( sometimes unfairly) about how hard it is to tie-up sequence data from NCBI with protein data from Swissprot and Uniprot. I just saw this on the gene announce mailing list “ In collaboration with UniProtKB  (http://www.pir.uniprot.org/) ,  the RefSeq group is now  reporting explicit cross-references to Swiss-Prot and  TrEMBL proteins  that correspond to a RefSeq protein. These correspondences are being calculated by the UniProtKB group, and will be updated every three weeks to correspond to UniProt’s release cycle. The data are being made available  from several sites within NCBI: “ This is a very nice development. I have always tended to look at the cross-references from within NCBI records for information on swissprot ids. But ... The Omics world blogs http://www.medworm.com/rss/comments.php?id=925293 Wed, 03 Oct 2007 17:11:39 +0100 925293 http://www.medworm.com/index.php?rid=921768&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F164455091%2F At the risk of beating on a dead horse; the utility computing space gets more crowded. Of course, still no sign of biotech jumping onto the boat Technorati Tags: Utility Computing, Biotechnology (Source: business|bytes|genes|molecules) business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=921768 Wed, 03 Oct 2007 00:35:15 +0100 921768 http://www.medworm.com/index.php?rid=916149&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F163582908%2F I have previously written about 3Tera, a company provides other companies with an infrastructure for on-demand computing. Read/Write Web, which pointed me to 3Tera in the first place, has a new post about 3Tera getting into online gaming. However, it is the rest of the post that caught my attention. Back in the day, we had to purchase supercomputing time and then run jobs till you ran out of your allocation. In todays world you can purchase time as you go along. Companies like 3Tera, Amazon, Google, Sun, IBM, etc have infrastructure that supports on demand computing. However, in the scientific world, we have not really started to take advantage of all these computing resources. Nor have we begun to look at the existing large scale computational infrastructure as an on demand cloud. In a w... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=916149 Mon, 01 Oct 2007 06:11:55 +0100 916149 http://www.medworm.com/index.php?rid=906110&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F161533625%2F I have written previously about Google’s interest in large scientific datasets. Attila Csordás, who earlier wrote about dark data, followed up with Jon Trowbridge at Google about Google’s efforts in this direction. While the talk from Scifoo is not available, Attila got permission to upload Jon’s talk up on Slideshare. The presentation is quite similar to the talk at Scifoo, and should give you a good idea about Google’s efforts, specifically the drive array that I talked about in my original post. One line from the presentation jumps out at you Ultimate goal: Promiscuous distribution The way I look at it, Google is saying this - we have the hardware; it doesn’t cost us much, so send it across to us and we will hold it, but not just for you. To me and oth... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=906110 Wed, 26 Sep 2007 14:01:08 +0100 906110 http://www.medworm.com/index.php?rid=894221&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F160445572%2F In a post some months ago, I had used the following quote Data finds data, then people find people I had mentioned that the originator of the idea that “data finds data” was Jeff Jonas. I had the pleasure of meeting Jeff at Scifoo, where we spent a brief amount of time talking about his theories on data and the applications in bioinformatics. I’ve spent some time in recent days devouring his blog. One of the statements from there that really made an impact on me Sensing importance across a sea of dynamic systems with constantly changing data requires the accumulation and persistence of context. This statement has a lot of applications in the life sciences. Let’s take the example of a project at a biotech or pharma company. The project contains information from m... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=894221 Mon, 24 Sep 2007 04:12:39 +0100 894221 http://www.medworm.com/index.php?rid=885366&cid=t_104570_132_f&fid=35014&url=http%3A%2F%2Fharijay.wordpress.com%2F2007%2F09%2F19%2Fthe-rich-pdb-interface-explained%2F It was a while back that I caught the video on the PDB site which explained all the functionalities that its search interface has. Thanks to the screencast I became a much more efficient querier of the PDB,  especially after they adopted the new ( now almost three years old) interface. I strongly believe that screencasting can play a role in helping us all search better. Since I work on crystallizing  membrane proteins , I found the MPDB very useful and decided to screencast its  features. I sincerely hope that  database creators, and users alike, take to this effective medium and screencast their tips and tricks for us all to benefit from. . (Source: The Omics world) The Omics world blogs http://www.medworm.com/rss/comments.php?id=885366 Wed, 19 Sep 2007 21:45:29 +0100 885366 http://www.medworm.com/index.php?rid=877652&cid=t_104570_132_f&fid=35014&url=http%3A%2F%2Fharijay.wordpress.com%2F2007%2F09%2F17%2Fwhy-are-our-bioinformatics-workflows-so-complicated%2F Last week to answer one question I had to resort to information from several sources . A lot of them contributed immense value to my “workflow” and were also either difficult to perform or very easy. For a start I have ranked them in terms of both Value ( 1 for no value to 10 for a lot of value) to ease of use ( 1 for very complicated to 10 for very easy) # Assembling my sequences in DNAstar (Value 10 : Ease 7 ) # Compiling my sequences and pulling them into Jalview. Ran CLUSTALW web service on edited alignments and realized that all of my clones had basically two sequences for their CDRs . . Jalviews excellent web-service CLUSTALW interface allowed me to quickly edit the 32 sequences , align them interactively and realize they belonged to two types. This got me thinking that... The Omics world blogs http://www.medworm.com/rss/comments.php?id=877652 Mon, 17 Sep 2007 16:03:16 +0100 877652 http://www.medworm.com/index.php?rid=874954&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F157096368%2F Via Bioinform (sub required). The German Ministry of Research is funding a project to model the transport of drugs into the liver. This is just another example of a trend to use in silico systems for predictive modeling of living systems. Of all the areas of life science, perhaps even more than search, it is biosimulation that really gets me excited. Just the possibility of building artificial patients and realistic models of the human body is just fascinating. Technorati Tags: Biosimulation, Predictive Modeling (Source: business|bytes|genes|molecules) business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=874954 Sun, 16 Sep 2007 07:00:26 +0100 874954 http://www.medworm.com/index.php?rid=872160&cid=t_104570_132_f&fid=35014&url=http%3A%2F%2Fharijay.wordpress.com%2F2007%2F09%2F14%2Fthe-restful-ncbi-query%2F I first caught this on Pierres blog. NCBI it turns out can be queried along REST principles ( hence the RESTful in the title). Ever since learning about REST-based URLs , I always wished that many web APIs implemented the ideology in their design. I was excited to learn how easy and intuitive it becomes to query a database using REST principles. Gone are queries that looked like http://www.ncbi.nlm.nih.gov/sites/entrez?db=homologene&cmd=search&term=dystrophin And here come queries that look like this http://view.ncbi.nlm.nih.gov/homologene/search/dystrophin  which look for genes that have homology to dystrophin. Several of the web APIs like the one for connotea and del.icio.us are also implemented RESTfully, making them very easy to query. For eg to get all entries on connotea or ... The Omics world blogs http://www.medworm.com/rss/comments.php?id=872160 Fri, 14 Sep 2007 17:46:27 +0100 872160 http://www.medworm.com/index.php?rid=872178&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F156453449%2F Salesforce.com will be entering the custom software market with Force. The Force is a platform that will allow developers to create database driven applications and deploy them as services. This is in line with other recent efforts in this area such as Coghead or DabbleDB I often wonder if such a trend will ever happen in the life science space, where companies or research groups will create similar application frameworks, with scientific data awareness of course, which can then be leveraged by others to deploy data-dependent services, either internally or public/customer facing. To use a really bad example, since it’s not going to happen, the NCBI could develop a rich development framework around their data sources, and application developers could then develop and deploy hosted ser... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=872178 Fri, 14 Sep 2007 14:41:33 +0100 872178 http://www.medworm.com/index.php?rid=870459&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F156437472%2F Via The HealthcareIT Guy. A conference on demonstrating open source healthcare IT solutions would be interesting to attend. The conference is part of the SoCal Linux Expo. If I had still been in SoCal, might just have done exactly that. Technorati Tags: Open Source, Linux, Healthcare, Healthcare IT (Source: business|bytes|genes|molecules) business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=870459 Fri, 14 Sep 2007 13:51:52 +0100 870459 http://www.medworm.com/index.php?rid=869532&cid=t_104570_132_f&fid=35014&url=http%3A%2F%2Fharijay.wordpress.com%2F2007%2F09%2F13%2Fncbi-oddities%2F I have often blogged about my trials and tribulations with the NCBI database.This morning I was trying to locate all the kappa light chain genes from the NCBI database. I tried the following search Immunoglobulin kappa mouse in the Genome database subsection. The results I got were a curious mix of microbe genomes ranging from Aspergillus Niger to Salmonella enterica. Maybe I left my search skills at home or my eyes are playing tricks on me. Addendum: Eric Jane from Uniprot showed me how to do the same query on Uniprot beta. Uniprot really rocks. Not only could I do the query , but also downloaded the results in batch mode as fasta sequences and in the xml format.Thanks eric , I would definitely recommend uniprot beta to everyone. Isabelle phan from uniprot did post an excellent screencast... The Omics world blogs http://www.medworm.com/rss/comments.php?id=869532 Thu, 13 Sep 2007 22:34:51 +0100 869532 http://www.medworm.com/index.php?rid=852533&cid=t_104570_132_f&fid=35014&url=http%3A%2F%2Fharijay.wordpress.com%2F2007%2F09%2F08%2Fsequence-first-ask-questions-later%2F I am little confused after reading about the metagenomics approach that identified the causative agent for the colony collapse disorder which Deepak and myself blogged about. After trolling through pubmed , it seems like a number of the honeybee potential pathogens were already quite well known. The Kashmir bee virus and the Israeli acute Paralysis virus were also lurking among bee populations. Was is not then possible to query this with a quick microarray designed following some text and sequence mining . Or maybe its just faster to just sequence the whole bee and then perform the in vitro RT-PCR experiments which are a little more targeted. Maybe this does say something about the difficulty of on the fly bioinformatics driven microarray fabrication . Since the closest I have come to a mi... The Omics world blogs http://www.medworm.com/rss/comments.php?id=852533 Sat, 08 Sep 2007 17:54:26 +0100 852533 http://www.medworm.com/index.php?rid=849992&cid=t_104570_132_f&fid=35014&url=http%3A%2F%2Fharijay.wordpress.com%2F2007%2F09%2F07%2Fmetagenomics-gives-clues-to-a-three-year-problem-affecting-bees%2F Just yesterday I was reading about how metagenomics is proving to be a better choice for many questions than many traditional DNA amplification centric molecular techniques like many microarray and other PCR based approaches. Metagenomics , which is a fancy way of saying ” sequence everything ” directly from the sample and then figure out what that everything is , now has another feather in its cap , the identification of the possible causative agent for the honeybee colony collapse disorder. CCD is a scary disease which has been affecting bee populations across the US . CCD is the name given to the end result , a colony of bees collapses because almost its entire adult bee population essentially disappears. The collapsed hives have the queen bee and a few newly emerged adult b... The Omics world blogs http://www.medworm.com/rss/comments.php?id=849992 Fri, 07 Sep 2007 16:23:22 +0100 849992 http://www.medworm.com/index.php?rid=838101&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F151705323%2F If you are a scientific software startup with just a few people, or an informatics service company with hosted software and/or content, working in a co-working situation and using computing services from a company like Amazon, Sun, and or Rackspace can go a long way. You don’t even need to chase down other bioinformatics companies, since you can share resources with other tech startups. This has me thinking. There are very few life science (or other science) companies that have ridden the current web startup craze (might be too late now). Compared to the number of bioinformatics/modeling companies that came up in the late 90’s, new ones today are pitifully few although there are some that do look cool (e.g. NextBio), they still follow mostly traditional models while leveraging ... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=838101 Mon, 03 Sep 2007 17:37:17 +0100 838101 http://www.medworm.com/index.php?rid=836445&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F151087302%2F I am on bit of a roll here, going outside my usual safe topic comfort zone. Nothing against TimeLogic, but tell me why I would purchase something like the CodeQuest workstation? From the product description page The CodeQuest™ workstation combines optimized algorithms, powerful hardware acceleration, and PipeWorks™ visual workflow software to drive your genome exploration and drug discovery research. CodeQuest is an effective solution for bioinformatics experts and novices alike. You can build and process genomic analyses without tedious scripting, achieve compute-cluster performance, all in a desktop solution that can be shared by the entire lab. Turnkey solutions have never worked in the life sciences (I can’t think of a single successful example), and in a world where I can ... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=836445 Sun, 02 Sep 2007 00:14:01 +0100 836445 http://www.medworm.com/index.php?rid=833433&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F150399331%2F I’ve always wondered how useful Amazon’s EC2 service could be for scientific applications. It should be interesting to see how the this proteomics project turns out Technorati Tags: Amazon, EC2, Life Science (Source: business|bytes|genes|molecules) business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=833433 Fri, 31 Aug 2007 05:51:07 +0100 833433 http://www.medworm.com/index.php?rid=828181&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F149497121%2F Interested in Accelerated Computing? Do you use FPGA’s or other novel architectures for scientific computing? You have to read this post (and comments) on the Accelerated Computing meme by Joe Landman and another where he talks about the future of high performance computing. I’ve always struggled with the role of accelerators for scientific computing. The geek in me loves the concept, but as raw processing power in computers has improved, the sheer convenience of clusters, and increasingly of computing out in the cloud just seems more appealing. At some point though, we will hit the architecture limits that Joe talks about. What kind of architectures will we be using then? Will we have to rewrite all our code? These are just some of the questions that will need to be answered b... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=828181 Wed, 29 Aug 2007 04:59:52 +0100 828181 http://www.medworm.com/index.php?rid=814242&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F146708107%2F Kaitlin Thaney, whom I had the pleasure of meeting at Scifoo, has a post up at the Science Commons blog where she points to an article on a Cyberinfrastructure for Knowledge Sharing, where John Wilbanks (also from Science Commons) writes about the importance of infrastructure for knowledge sharing. The article focuses on the life sciences, where converting data to knowledge, knowledge that can impact human lives, is a constant challenge. I completely agree with John when he says that “we need the Web to work as well for science as it does for other areas.” Science, which was instrumental in the mere existence of the web, has fallen back in many ways. While a lot of pharma and biotech companies, academic institutions, etc use the web extensively for science, I have always felt t... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=814242 Wed, 22 Aug 2007 00:11:44 +0100 814242 http://www.medworm.com/index.php?rid=790595&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F142515536%2F GIVE US YOUR DATA!!! Yes that was the title of a session led by Google-ites, including Chris DiBona (I forget the name of the actual session leader). The following are notes from that session, somewhat cleaned up. Google has a mission, one of organizing the worlds information and making it universally accessible and useful. In keeping with that mission, it should come as little surprise that they have a tremendous interest in the sciences. Their current project has the following goals 1. Archive interesting scientific data 2. Distribute data to the people who need it At this point, they would essentially like to solve engineering infrastructure problems, in a world where the cost of storage is going down by 78% every year. (”Moore’s law is for wimps” was the title of tha... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=790595 Thu, 09 Aug 2007 21:49:45 +0100 790595 http://www.medworm.com/index.php?rid=751731&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F136558285%2F (Via Bioinform). ZOOM*UserViews is a formal model of provenance for scientific workflows. Sounds like a mouthful doesn’t it. I was trying to figure out what that meant, but if you read carefully, you get the drift. There are many scientific workflow systems out there. The site mentions Kepler, myGrid/Taverna and Chimera, but you can add commercial workflow engines to this list as well. These systems are very powerful, and many companies and institutions use them as a means to capture best practice. There are some open questions that remain. For example you might want to know the means by which the data were produced. ZOOM*UserViews essentially tries to tackle this problem, one that leads to issues with data interpretation and usability. How does it achieve jthat? As mentioned earlie... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=751731 Mon, 23 Jul 2007 17:09:18 +0100 751731 http://www.medworm.com/index.php?rid=742625&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F134948684%2F Curating annotations in for biological informatics is hard. There are companies that have many people searching through literature looking for protein-protein interactions and other similar relationships. A large part of what makes some databases more attractive is the level of curation, manual or otherwise. What if we could change the way that this goal is achieved, perhaps via some of the same resources that we are using the tech world? Many of us have talked about Freebase and its possibilities. Earlier today I was reading up a little on Phrasetrain, a local Seattle company that is using peer production to create a natural language technology. I am not quite sure how it works, although I have signed up for the beta. From their About page (emphasis mine) Phrasetrain is a small new techno... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=742625 Wed, 18 Jul 2007 14:30:03 +0100 742625 http://www.medworm.com/index.php?rid=736317&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F134199385%2F This blog is supposed to be at the interface of biology and information technology. Well I have seen few example at that interface in recent days that beat Planet Nature. Planet Nature is the portal to all the Nature blogs. I love the clean interface and the ability to access individual feeds if required. It takes advantage of Google Custom Search (I should probably add Planet Nature to my Lijit Wijit). Here is the killer though, especially for the geek in me. Alf has implemented an RSS filter. Enter a keyword and click and filter, and voila, you land up on a Yahoo Pipes page. Way cool!!! The filter checks the RSS feed for any keywords and you can then subscribe to the results. I just subscribed to a couple. As an aside, you can tell who might be behind the pipes from the avatar on the top... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=736317 Mon, 16 Jul 2007 13:07:01 +0100 736317 http://www.medworm.com/index.php?rid=733676&cid=t_104570_132_f&fid=35014&url=http%3A%2F%2Fharijay.wordpress.com%2F2007%2F07%2F13%2Fback-on-the-ncbi-horse%2F I have been working a lot with alignments in Jalview and had blogged about how Google can find Uniprot IDs better than NCBI ..well it turns out that NCBI did indeed have most of the Uniprot sequences I was looking for. The fault was mine! for not using the correct form of uniprot id.. The catch I had to say just Q57T52 instead of the Q57T52_SALCH and Q325Y4 instead of Q325Y4_SHIBS Which brings to me to one incredible thing about google. The google suggest and spelling correction. NCBI recently added the spelling correction feature. But still does not have something that would have told me that I should try Q57T52 instead of the old style Q57T52_SALCH uniprot id query. So all in all out of the 742 sequences that the manually curated PFAM database had used in its voltage_clc gamily alignmen... The Omics world blogs http://www.medworm.com/rss/comments.php?id=733676 Fri, 13 Jul 2007 20:51:13 +0100 733676 http://www.medworm.com/index.php?rid=733812&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F133351596%2F An interesting case study popped up in my inbox today. The title, albeit clichéd, is provocative enough. Knowledge discovery, search, etc are common themes in the bioinformatics blogosphere, and over the years I have seen many companies develop decent, but usually non-innovative methods to search and mine biological data. Why are the available solutions not quite good enough? And what does it really mean to be the “Google of bioinformatics”? Those are the questions that popped up in my head as I read through the case study. The lack of good solutions is easily explained. The first thing that came to mind was that a “Google” for bioinformatics would not be just be an improvement over current techniques, but rather an approach that leapfrogs everything available and ... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=733812 Fri, 13 Jul 2007 13:27:16 +0100 733812 http://www.medworm.com/index.php?rid=710290&cid=t_104570_132_f&fid=35014&url=http%3A%2F%2Fharijay.wordpress.com%2F2007%2F07%2F02%2Fexciting-times-on-the-science-web-timo-hannay-on-nascent%2F I was very excited to read Timo Hannays post on the Nature Nascent blog where he reproduced an excerpt from his post for STM news on “how Oreilly and the alpha-geek crowd have influenced Nature Magazine”. Titled , web opportunity , the post talks about the great opportunities that lie in the web for all of science and science publishing. In the very interesting post Timo talks about the democratization of audio and video and Natures experiments with the Nature podcast. The Nature podcast apparently started off as just an experiment and then grew to almost 30,000 downloads at the end of its first year. The article talks about scientists who listen to the podcast when they are on the microscope and commuting in or exercising. In my own case, I find that thanks to the nature podca... The Omics world blogs http://www.medworm.com/rss/comments.php?id=710290 Mon, 02 Jul 2007 18:25:22 +0100 710290 http://www.medworm.com/index.php?rid=705917&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F129167024%2F I first started writing this post when L’Affaire Avandia first came to light, but decided to put it off this the incessant coverage had died down. Of course, days became weeks, but better late than never. I will not focus on the specifics of the Avandia situation, but rather on the concept of pharmacovigilance and the role of post-marketing analysis, at least as far as I understand the problem. Listening to a lot of talks on adverse event reporting at the DIA conference also definitely helped crystallize some of these thoughts. In the recent NEJM paper, Steve Nissen and Kathy Wolksi essentially carried out a meta analysis, where they combined results from multiple independent studies (42 clinical trials) to arrive at their conclusions. That got me thinking. What constitutes appropria... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=705917 Sat, 30 Jun 2007 05:07:07 +0100 705917 http://www.medworm.com/index.php?rid=704491&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F128980548%2F Just a note about a trend I have noticed recently. A few years ago, being a life science content company was usually equal to certain failure as a business. In the past year though, I’ve noticed content companies make a comeback, often as Software as a Service companies. Will be interesting to see how they fare. The market can only bear so many providers. Technorati Tags: Bioinformatics, Content Providers, SaaS (Source: business|bytes|genes|molecules) business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=704491 Fri, 29 Jun 2007 14:30:21 +0100 704491 http://www.medworm.com/index.php?rid=703096&cid=t_104570_132_f&fid=35014&url=http%3A%2F%2Fharijay.wordpress.com%2F2007%2F06%2F28%2Fbioscreencastcom-screencasting-for-the-life-sciences%2F For the last many months five of us have been toiling away at building a tool for the life sciences. I am very excited to announce bioscreencast.com , our attempt at building a community for the Life Science sciences. As biology gets more and more complex. We all found that we were forced to wear many hats. The march of genomics into every area of life science, forces us to learn new skills everyday.  There is no denying , how every life scientist has to become very well versed with computational data analysis. The lines between the former day computational biologists , bio-informaticians , statisticians, crystallographers, theoreticians and bench life scientists are blurring everyday. Bioscreencast.com is our attempt at building a community that can share its knowledge through the powerf... The Omics world blogs http://www.medworm.com/rss/comments.php?id=703096 Thu, 28 Jun 2007 20:36:33 +0100 703096 http://www.medworm.com/index.php?rid=695318&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F127953296%2F Bora writes In other words, Science 2.0 is scattered all over. I have far too many bookmarks to various sites and I cannot and will not check every one of them every 10 minutes. But if there was ONE SINGLE place to go and get all of the stuff, it would be a site of choice to every scientist on the planet. By now you must have guessed that I am not quite in agreement. I think science belongs in a distributed world, in blogs, in journals, in places like Precedings. Too much centralization never did anyone any good anyway. The challenge is taking that information, mining it, searching it, aggregating it and making sense out of it. That’s where the challenge lies. That’s where the semantic web is going to make a huge impact. Aggregators like Scintilla are one approach, but I thin... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=695318 Tue, 26 Jun 2007 04:13:55 +0100 695318 http://www.medworm.com/index.php?rid=694201&cid=t_104570_132_f&fid=35014&url=http%3A%2F%2Fharijay.wordpress.com%2F2007%2F06%2F25%2Fnature-precedings-a-great-offerring-from-the-npg-stable%2F Nature just launched Nature precedings , a  home for Pre-publication research and preliminary findings. Within seconds of browsing through its very intuitive interface I immediately got the purpose of this offering from Nature Publishing group. The way it works is simple-  you can upload content in the form of word documents , powerpoint files and pdf files and it gets released to the community after a preliminary check for appropriateness of content and suitability for the nature precedings audience. Signed up users can then vote on the content ( a la Digg) and it gets moves up or down its category. All of the content is also search-able and link-able and citeable. As the help pages suggest, I hope the site serves , in the least as a repository of supplementary material and sc... The Omics world blogs http://www.medworm.com/rss/comments.php?id=694201 Mon, 25 Jun 2007 13:19:26 +0100 694201 http://www.medworm.com/index.php?rid=682876&cid=t_104570_132_f&fid=35014&url=http%3A%2F%2Fharijay.wordpress.com%2F2007%2F06%2F20%2Fwhy-google-may-be-better-to-find-uniprot-sequences-than-the-ncbi%2F My good friend Deepak had a quote in his blog from Lincoln Stein about making bioinformatics as much an everyday tool to the practicing biologist as a pipettor ( a device used to dispense liquids by experimental biologists and chemists).. I totally agree, but  think we are quite far away. For example this morning I had to obtain the sequence of 772 swissprot entries  ,which were part of  an alignment for some downstream analysis. Of course my first choice was to query the NCBI -Entrez database. I soon realized that NCBI query box did not return  any results for  the first few queries I tried, all of which were probably new Uniprot/SwissProt IDs ( for eg. .sequence ids Q57T52_SALCH ,Q325Y4_SHIBS ) Disappointed , I turned to the EBI search engine. Within seconds I re... The Omics world blogs http://www.medworm.com/rss/comments.php?id=682876 Wed, 20 Jun 2007 18:59:42 +0100 682876 http://www.medworm.com/index.php?rid=658928&cid=t_104570_132_f&fid=35014&url=http%3A%2F%2Fharijay.wordpress.com%2F2007%2F06%2F05%2Ferror-bars-and-experimental-biology-and-the-bbgm-podcast%2F I will try to keep this post real short. The Journal of Cell Biology carries a very useful article on error bars in experimental biology. Sadly the article is only available with a subscription, but here is a link to the abstract on pubmed. The article talks about error bars in different context and how they should be used. Targeted at the non-statistics geek the article is easy to follow and quite useful. My good friend Deepak who got me into blogging , recently started podcasting. Like his excellent blog the bbgm podcast is mostly about technology and computing and other things biotech . Deepak is extremely well plugged-in to the web 2.0 world and his podcast is fun medley of the things that catch his attention and the biotech-Bio IT business world . Recently he interviewed me on the fif... The Omics world blogs http://www.medworm.com/rss/comments.php?id=658928 Tue, 05 Jun 2007 15:31:37 +0100 658928 http://www.medworm.com/index.php?rid=654483&cid=t_104570_132_f&fid=35014&url=http%3A%2F%2Fwww.nature.com%2Fnature%2Fpodcast%2Fv443%2Fn7110%2Fnature-2006-09-28.mp3 I have recently become addicted to the TED talks. I caught the TED talk by Craig Venter on various projects stemming from the initiatives undertaken by the Venter Institute and his affiliated companies. One of the exciting things he talked about was the coming field of combinatorial genomics (CG). CG is basically a marriage between synthetic biology and genomics. Basically it will deal with creating “synthetic” life forms with desired properties that are obtained by screening a library of such microbes obtained from combining genes from a multitude of organisms. This is of course possible given the following five technologies. Knowledge of a minimal subset: Work on the “minimal genome project” resulted in the minimal set of genes required to have a living reproducin... The Omics world blogs http://www.medworm.com/rss/comments.php?id=654483 Sun, 03 Jun 2007 07:48:30 +0100 654483 http://www.medworm.com/index.php?rid=651148&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F121547681%2F The first time I heard about Amazon’s EC2 service, I was struck by the thought that very soon a biotech company, with modest computing needs  would not need to have a datacenter with a big cluster, but rather use a service like EC2 to satisfy it’s computing needs.  A couple of weeks ago I asked Charlie Bell about EC2 and MPI, and guess what, it’s doable.  Jeff Barr blogs about EC2, Mpich2 and Blast. Perfect!!!  Now, mind you, if you are in the situation where you are crunching the entire human genome all the time, a dedicated cluster is worth it.  But if you are a company that usually runs small jobs and occasionally needs the big spike in compute power, the EC2/S3 combo is quite intriguing and I have a feeling it would be fairly cost effective. F... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=651148 Sat, 02 Jun 2007 04:00:47 +0100 651148 http://www.medworm.com/index.php?rid=645193&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F120795655%2F Interesting article in Bio-IT World on some of the impact that “Web 2.0″ applications can have on storage requirements at life science companies. As someone who shakes his head at how little life science companies take advantage of modern internet technologies and trends, I was a little skeptical of the premise of the article, and at the end of it, I must admit to being a little annoyed. The article talks about how web 2.0 applications, e.g. the practice of tagging image data, is requiring companies to plan their storage needs better. To some extent I can picture how this process works. In a very early life at a bioinformatics company, way before anything became 2.0, we used to capture a lot of metadata and do a lot of manual annotation of results. That in itself lead to the ne... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=645193 Wed, 30 May 2007 14:15:26 +0100 645193 http://www.medworm.com/index.php?rid=638229&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F119711436%2F From Bioinform (sub reqd) we learn about a proposal from Aaron Cohen and William Hersh of the Oregon Health and Science University’s Department of Medical Informatics and Clinical Epidemiology to develop a wiki-style thesaurus that would contain disease names, types, and variations. According to the scientists, the thesaurus would be based on a relational data model that connect all the data types. The goal of the project is to discover relationships and associations and eventually therapeutic mechanisms. The hope is to bring as many as 20,000 bioinformaticians and researchers into the project. From where I stand, just limiting the proposal to a relationship-oriented wiki might be too narrow. Here is what would be really cool 1. A wiki-style system as proposed built using a Freebase-styl... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=638229 Sat, 26 May 2007 01:11:26 +0100 638229 http://www.medworm.com/index.php?rid=638230&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F119199469%2F Yesterday, I blogged about Google’s financing of 23andMe, a company focussed on personal genetics. Keeping the Google and healthcare theme going, there is a post at the Google blog today by Adam Bosworth, where he talks about a speech that he gave at the AMIA spring congress. As is his wont, Adam includes his speech notes in the blog post (pdf). The focus of the talk is a vision of the future of healthcare, specifically personalized healthcare. In keeping with talks he has given in the past, Adam starts with the premise that consumers should own their own health and wellness data, and importantly how it is used. For example, if electronic records are moving between insurers and healthcare providers, a copy should reach the consumer as well. The three pillars of Google’s healthc... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=638230 Thu, 24 May 2007 05:02:30 +0100 638230 http://www.medworm.com/index.php?rid=629287&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F118313819%2F At the Bio-IT World conference earlier this year, Robin Spencer, Chief Idea Management Officer (don’t you love titles like that) and senior research fellow at Pfizer, gave a keynote entitled Drug Discovery 2.0: From Push to Pull. Talk titles like that carry a lot of weight in these parts. That his talk drew from Science Business further piqued my interest. So what was the talk all about? In two words - Idea Management. Or to be more precise, about new approaches to idea management for the pharma/biotech industry to be really successful. Spencer, channeling Gary Pisano argues that the life science business inherently lacks some of the features that lead to success in other industries, notably, scale, predictability and control. Then, and this is the part I love, Spencer says that what... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=629287 Mon, 21 May 2007 04:21:46 +0100 629287 http://www.medworm.com/index.php?rid=612383&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F117506867%2F Fascinating article by Nick Carr in the Guardian on how the internet has reached a stage that generates a big feedback loop, leading to the popular destinations on the web becoming even bigger. To some degree, I agree. It is natural human behavior to gravitate towards something that is popular and where the people you know are going. However at another level, I disagree, and perhaps that is just one man’s world view. To me, the internet, whether it be search, social networks, or what have you, is a means of serendipitous and not so serendipitous discovery. When I am looking for information about, e.g. “systems biology”, like everyone else, I check the top hits on google, but that is not the end. After that you scan down the list, add more specific keywords, try and find w... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=612383 Thu, 17 May 2007 18:37:23 +0100 612383 http://www.medworm.com/index.php?rid=612186&cid=t_104570_132_f&fid=35014&url=http%3A%2F%2Fharijay.wordpress.com%2F2007%2F05%2F16%2Fraindance-and-genomics-20%2F An interesting article in BioIT world talks about Jonathan Rothbergs ( the founder of 454 Life Sciences) keynote address to the Bio 2007 conference in Boston , where he talked about his future venture, called  Raindance technologies a “nanoreactor” company that seems to use a combination of microfluidics and “454 style” oil emulsion and quantum dot based optical analysis to create a highthroughput assay platform. The impressive set of videos at the raindance site explain the various steps of the assay platform. The adoption of quantum-dot based detection systems incorporated into their nano-reaction vessels makes it possible to conduct a wide variety of assays at an amazing throughput of several thousand reactions per second.The article talks of the possibility... The Omics world blogs http://www.medworm.com/rss/comments.php?id=612186 Wed, 16 May 2007 14:29:13 +0100 612186 http://www.medworm.com/index.php?rid=612386&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F117058435%2F A post by Peter Murray-Rust pointed me to one by Paul Miller with a detailed look at a panel discussion at the XTech conference (Cool web tech conferences in Paris .. hmmm). The panel was actually a Birds of a Feather (BOF), i.e. open to the public, session aimed at covering themes “important to those developing and promoting tools for scientific research, collaboration and publishing online”. The following items/thoughts jumped out at me from the two articles Publishers, or at least the ones who seem to get it, are in a healthy competition. Where I hope they don’t go their different ways is in implementing their own “standards”, cause however open a standard might be, it isn’t really a standard unless it gets wide adoption. Why does HTML still exist?... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=612386 Wed, 16 May 2007 05:49:25 +0100 612386 http://www.medworm.com/index.php?rid=612187&cid=t_104570_132_f&fid=35014&url=http%3A%2F%2Fharijay.wordpress.com%2F2007%2F05%2F15%2Facademic-plasmid-sharing-made-easy%2F While I was researching an article on opsins that are revolutionizing neuronal investigation, I came across a small blurb on the Boyden lab homepage with a link to addgene which said ” Request Boyden Lab plasmids through addgene”. Addgene as its webpage states is a non-profit research support service dedicated to archiving and distributing plasmids that appear in published articles.The plasmids in addgenes database are classified on the basis of the Principal investigator deposting them and gene name. Also each plasmid has a lot of detailed information available making its use in other experiments quite easy. It was very heartening that several leading labs had deposited their plasmids for academic use at this service. In the world of open science , services such as this are in... The Omics world blogs http://www.medworm.com/rss/comments.php?id=612187 Tue, 15 May 2007 16:55:17 +0100 612187 http://www.medworm.com/index.php?rid=590131&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F114187204%2F I was supposed to be at the Bio-IT World Conference in Boston earlier this week, but due to some critical projects at work, I had to pull out. So like anyone does these days, I’ve been scouring the web for blog posts about the actual happenings (i.e. something other than market copy and coverage by Bio-IT World itself). And so far I have been relatively unsuccessful at this attempt at vicarious living. The limited stuff I found An post by Dave Kellog, CEO of Mark Logic Corp. on MarkLogic Server being named a finalist for the Bio-IT World Best of Show awards. By the way, always nice seeing geeky blogging from company CEOs An announcement from Sun. Like the MarkLogic entry, this talks about a company’s product, but both are done in a bloggy sort a way, not just rehashed press sta... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=590131 Fri, 04 May 2007 17:26:56 +0100 590131 http://www.medworm.com/index.php?rid=556957&cid=t_104570_132_f&fid=35014&url=http%3A%2F%2Fharijay.wordpress.com%2F2007%2F04%2F20%2Fblogs-that-make-me-think-or-a-post-from-a-fan%2F Deepak , who introduced me to blogging recently added me onto his list of “Thinking bloggers”. I am honored to be part of a list on bbgm that contains four veteran bloggers and I am sure being his friend has a lot to do with it. I feel compelled to propagate the”meme” ( a term about which I knew nothing about till I read it on bbgm) . SO , If I am to list the blogs or bloggers that inspired me the list would go like this.. 1)Jon Udell : I started reading his columns in infoworld many years ago. But it was reading through reading his blog posts that got me interested in Screencasting ( he is the originator of the term) , XML , the seminars on long term thinking and about 95% of the things that take up my “free” time. 2) Chris Geminiani at Juice analytics:... The Omics world blogs http://www.medworm.com/rss/comments.php?id=556957 Fri, 20 Apr 2007 17:37:20 +0100 556957 http://www.medworm.com/index.php?rid=544262&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F109133740%2F I found out about Ali Baba via del.icio.us and a quick blog search showed that Joerg has already mentioned it before. So what is Ali Baba? According the the website “Ali Baba parses PubMed abstracts for biological objects and their relations as discussed in the texts. Ali Baba visualizes the resulting network in graphical form, thus presenting a quick overview over all information contained in the abstracts.” There is a lot more detail about the kind of information available on the About page. The list of features is quite large and appears to be quite useful. For example, you can visualize the known or suspected genes associated with Parkinson’s disease using a simple query like “parkinson disease genetic cause”. The result is the following graph The appli... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=544262 Sun, 15 Apr 2007 01:50:49 +0100 544262 http://www.medworm.com/index.php?rid=529750&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F107610081%2F Last night, at Ignite Seattle, I heard an excellent talk by Keith Schorsch, CEO of PeerWisdom, a new startup focusing on bring health information to consumers, based on Keith’s personal experiences. I think the field in general is due for a shot in the arm. I am not sure who will do it, or how. The dangers of confusing information are all too real, and as we gain more control of our own information, e.g. when genotyping individuals becomes sufficiently inexpensive, and molecular medicine becomes intrinsically related to patient care, then the problems are only going to become more complex. The challenge lies in bringing together medical and scientific expertise, individual experiences and data mining in such a way that allows individuals to have maximal knowledge about their conditio... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=529750 Mon, 09 Apr 2007 02:00:24 +0100 529750 http://www.medworm.com/index.php?rid=515190&cid=t_104570_132_f&fid=35014&url=http%3A%2F%2Fharijay.wordpress.com%2F2007%2F04%2F01%2Fmembrane-protein-crystallization-analytics%2F I am starting to really like analytics. I started following the developments in the “analytics movement “after reading about companies like juice analytics , swivel , gapminder and “many eyes” at the bbgm blog. Along these lines Nature magazine also recently carried a news and views piece on IBMs many-eyes and the opportunities it afforded for scientific collaboration. As a person closely involved in membrane protein purification , characterization and crystallization , I am always on the lookout for information related to the various aspects of doing membrane protein biochemistry . The very good compilation of membrane proteins of known structure compiled by Steven white at U.C Irvine was always my go-to place for information about membrane protein structures . Bu... The Omics world blogs http://www.medworm.com/rss/comments.php?id=515190 Sun, 01 Apr 2007 11:05:26 +0100 515190 http://www.medworm.com/index.php?rid=512530&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F105514908%2F Over the years, many information services companies, notably IBM and SAIC have been actively involved in working with the pharmaceutical industry in trying to develop IT solutions to improve business processes and develop the infrastructure for improved data handling in clinical trials, drug discovery, etc. Of course, much of the hardware that provides the computing resources for in silico drug development also comes from the IBMs and HPs of the world. Many of the services being provided include the development of knowledge management solutions for drug discovery and clinical trials. In recent years some other companies, not historically involved in the healthcare/drug development business, have become actively involved in the field. To an extent this is a natural evolution of a world wher... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=512530 Sat, 31 Mar 2007 03:31:08 +0100 512530 http://www.medworm.com/index.php?rid=511400&cid=t_104570_132_f&fid=35014&url=http%3A%2F%2Fharijay.wordpress.com%2F2007%2F03%2F30%2Fblink-and-its-done%2F The Blink database at the NCBI The NCBI which I have blogged about before has a number of outgoing links embedded into its search results. One of these links which I use extensively is the Blink-link , which is basically a precompiled BLAST run . The BLAST link - blink exists for every annotated sequence in the database and is a great way to look at homologs to any given sequence without messing around with cutting and pasting sequences into web forms or BLAST input parameters. As easy as clicking on a link- the results come nicely laid out with all the homologs color coded by taxonomy , i.e the archaea , bacteria , fungi , plants , etc. Clicking on any graphic takes you to the pairwise alignment. Clicking on a GI ( a unique numeric ID for every sequence in the database) takes you to the ... The Omics world blogs http://www.medworm.com/rss/comments.php?id=511400 Fri, 30 Mar 2007 18:29:48 +0100 511400 http://www.medworm.com/index.php?rid=500144&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F104324574%2F Things I noticed is back. Hopefully between this series, the podcast and regular blogging, most of the relevant stuff that catches my eye will get covered. HHS and personalized medicine The first thing I want to talk about today is the news that the Department of Health and Human Services (HHS) is making a concerted thrust in the area of “personalized medicine”. In addition to the funding plans, the part that caught my eye was the plan to develop a “network of networks that pulls together health care information from the nations major health data repositories to enable researchers to match treatments and outcomes.” For more see the HHS personalized healthcare website … meanwhile cancer funding is in dire straits While I laud the HHS for the increased attention to... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=500144 Sun, 25 Mar 2007 18:34:48 +0100 500144 http://www.medworm.com/index.php?rid=490872&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F103577468%2F Via Techmeme I found this short post by Dave Winer in which he quotes Peter Rip The Web today still resembles MS-DOS more than MS-Windows. Every website is an island, an island that knows nothing about any other website. This is no different than the world before the Windows Clipboard. All 640KB of memory was available to whatever application was running. The point of integration was the User. As it is today. This quote really hits home. With exceptions the world of biological information is exactly that, an island. The integrated web of information is a misnomer. Just because Google indexes the web doesn’t make it integrated. So how does this change? That’s why I am intrigued by the semantic web, Freebase, microformats, etc. In the software business we talk about about develop... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=490872 Thu, 22 Mar 2007 16:11:54 +0100 490872 http://www.medworm.com/index.php?rid=486933&cid=t_104570_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F101029398%2F At the recent US HUPO conference, I happened to walk by a poster entitled “ProteomeCommons.org Tranche: Publicly storing and sharing large amounts of proteomics data”. I ended up having a short chat with the developer of Tranche, Jayson Falkner and was quite impressed with the effort. What is Tranche? Let me quote the poster introduction. The ProteomeCommons.org Tranche project is designed to allow publication of all raw data relating to proteomics experiments. The system allows investigators to securely share files with collaborators, reviewers of manuscripts, and to publicly disseminate their data. Encryption and digital signatures allow authentication of data files, so provenance and integrity are unambiguous. The system provides for distributed downloads, background file c... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=486933 Mon, 12 Mar 2007 04:04:09 +0100 486933 http://www.medworm.com/index.php?rid=485790&cid=t_104570_132_f&fid=35014&url=http%3A%2F%2Fharijay.wordpress.com%2F2007%2F02%2F03%2Fwhy-i-think-the-ncbi-rocks%2F A while back I had written about how the NCBI had probably mis-indexed a particular protein domain annotation , because their search algorithm yielded irreproducible and probably erroneous search results for a particular search pattern (see Whassup NCBI) . Back then I had contacted the NCBI support staff who were extremely helpful and helped me initially troubleshoot the problem to some extent but told me I had to wait for the possible mis-indexing error to get corrected. A few after my initial post I got an email from NCBI support asking me if the problem persisted and whether I had tried repeating the search. I tried repeating the search and the problem had indeed been rectified. Throughout the whole process I had the good fortune of speaking one on one , with several of the support staf... The Omics world blogs http://www.medworm.com/rss/comments.php?id=485790 Sat, 03 Feb 2007 18:21:08 +0100 485790 http://www.medworm.com/index.php?rid=485792&cid=t_104570_132_f&fid=35014&url=http%3A%2F%2Fharijay.wordpress.com%2F2006%2F12%2F11%2Fcompiling-search-strategies-in-the-biosciences%2F  This morning I spent nearly two hours trolling through the various biological databases trying to find some information but in the end my searches drew a blank. I grew dejected at having wasted all that time only to find nothing. I then read Jon Udells blog post “Hunting the elusive search strategy” .  In this post , he talks about how some of us are  good searchers vs other people who are not.  He also says “Effective search depends on reservoirs of tacit knowledge and unconscious skill. Some people possess much deeper reservoirs, and/or can tap into them more effectively, than others. That makes them valuable.” Some have the ability to compile and relate matches and near matches on the fly  during a search to interactively synthesize a search strategy. Assum... The Omics world blogs http://www.medworm.com/rss/comments.php?id=485792 Mon, 11 Dec 2006 19:40:44 +0100 485792 http://www.medworm.com/index.php?rid=485793&cid=t_104570_132_f&fid=35014&url=http%3A%2F%2Fharijay.wordpress.com%2F2006%2F12%2F11%2Fsearch-in-this-omics-age%2F Often in the membrane protein world , we attempt to clone and express proteins from the microbial world , which are homologous to a particular human protein. Typically we identify a homolog of interest using BLAST and then try and PCR out the gene from genomic DNA from that particular homolog. Just this morning I wanted to attempt to clone out a homolog for a gene we study here in the lab from the bug yersinia pseudotuberculosis. The first step I followed was to look for the genomic DNA for the bug in the ATCC collection which is as its logo says ” A Global Bioresource center”. Using a simple word lookup among all the collections at the ATCC I found a list of 22 entries - success. This list informed me that the same bug was deposited into the ATCC under several different names.... The Omics world blogs http://www.medworm.com/rss/comments.php?id=485793 Mon, 11 Dec 2006 18:52:14 +0100 485793 http://www.medworm.com/index.php?rid=485795&cid=t_104570_132_f&fid=35014&url=http%3A%2F%2Fharijay.wordpress.com%2F2006%2F10%2F31%2Fthe-coming-deluge-google-buys-jotspot%2F Just caught this on the Google blog . Google buys jotspot. I have previously talked about the wonders of jotspot and the ability to virtualize , collaborate and share using the service and other Wikis like backpackit. With Google acquiring jotspot , I am sure we are very close to seeing a fully integrated experience with shared documents, spreadsheets and enterprise wiki features from the google-jotspot team. Maybe I might just move my “self ELN” away from backpackit to the new Jotspot. For now Jotspot has disabled further registrations and sent its users an email explaining that “Google shares JotSpot’s vision for helping people collaborate, share and work together online. JotSpot’s team and technology are a strong fit with existing Google products like Googl... The Omics world blogs http://www.medworm.com/rss/comments.php?id=485795 Tue, 31 Oct 2006 18:19:51 +0100 485795 http://www.medworm.com/index.php?rid=485796&cid=t_104570_132_f&fid=35014&url=http%3A%2F%2Fharijay.wordpress.com%2F2006%2F10%2F22%2Fscreencast-101-windows-media-encoder%2F I have recently learned quite a few features of the NCBI site which were hardly obvious to me. In the screencast below I explore two of these features. The History feature to combine searches and the “CDS” and “Reverse complement” feature to get at the reverse complement of a genbank ORF (open reading frame) record . The screencast was made on my macbook-pro laptop running parallels and Windows Media Encoder 9.0 from Microsoft (WME) on Windows XP Pro. WME is very easy to use and FREE software. The wmv file it output was sufficiently small (1.60 MB) and needed no additional tinkering. Sadly the Mac and OS X does not come with any free tools to make screencasts. I did give IshoU for Mac a shot, but the movies were very large files (10 plus MB) and I needed quicktime-p... The Omics world blogs http://www.medworm.com/rss/comments.php?id=485796 Sun, 22 Oct 2006 18:07:23 +0100 485796 http://www.medworm.com/index.php?rid=485797&cid=t_104570_132_f&fid=35014&url=http%3A%2F%2Fharijay.wordpress.com%2F2006%2F10%2F19%2Fa-blog-ressurected-screencasting-a-great-thing%2F After my previous post, I had a slew of computer troubles that left me out in the cold. My experience has thought me more than anything else to “virtualize” to the maximum extent possible . So I have moved towards keeping almost all my data off-site  on Backpackit  and various google services. In the future following a computer hardware failure I should be up and running the moment I have access to a browser running firefox. Getting back on track: My newest fixation along the lines of my post on Empressr is with screencasting. I stumbled on Empressr as I was looking for ways to present my data online and durig this search came across screencasting via movies explaining the use of the website Backpackit. John Udell from Info world, who also coined the term, has an excellent l... The Omics world blogs http://www.medworm.com/rss/comments.php?id=485797 Thu, 19 Oct 2006 23:42:46 +0100 485797 http://www.medworm.com/index.php?rid=485798&cid=t_104570_132_f&fid=35014&url=http%3A%2F%2Fharijay.wordpress.com%2F2006%2F09%2F28%2Fmoving-elns-offsite%2F I have been experimenting with several web based organization tools mostly to keep my research activities running smoothly. The service I use most often is Backpackit. On Backpackit, I have a separate page for each of my research projects. Ever project page has a series of notes describing daily experiments and all associated files and documents are neatly organized at the bottom. I also share these pages with collaborators and research technicians. All of who periodically update and annotate the content and rely on it to keep their own information in-sync. The ultimate aim apart from using them an organizational tool is to publish all of this. In Backpackit, these pages which are presently shared by only a few researchers can be made fully public and viewable to one and all. At that point... The Omics world blogs http://www.medworm.com/rss/comments.php?id=485798 Thu, 28 Sep 2006 14:42:40 +0100 485798 http://www.medworm.com/index.php?rid=485799&cid=t_104570_132_f&fid=35014&url=http%3A%2F%2Fharijay.wordpress.com%2F2006%2F09%2F27%2Fgreat-software%2F Warning non omics tangent ahead. Its been a whole two months since my last post. In the last few months I have had a unix laptop hard-drive crash and its reiserfs file system irrecoverably “trample on itself ” , a windows XP installation get corrupted and loose all video performance after a system update, and both of this resulted in my buying myself a macbook pro running OSX . These experiences made me ask myself that while I struggle with understanding protein structure and function correlations in my professional life, why cant engineers and scientists who deal with the vastly more predictable world of technology, build machines or systems that just do the right thing ( alright I use this apple add-speak because I just love OSX so far). I then paused to ask myself , which ar... The Omics world blogs http://www.medworm.com/rss/comments.php?id=485799 Wed, 27 Sep 2006 20:17:38 +0100 485799