MedWorm.com provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'Public Rambling' source. Mon, 17 Nov 2008 22:53:35 +0100 http://feeds.feedburner.com/~r/pedrobeltrao/~3/451287780/open-science-just-do-it.html My blog is 5 years old today and to celebrate I am trying to actually do some blogging. There are a couple of reasons why I have blogged less in the past months. In part it was due to FriendFeed and also in part because I was trying to finish a project on the evolution of phospho-regulation in yeast species. Nearing the end of a project should actually provide some of the most interesting blogging material but I did not ask for permission from everyone involved to write about ongoing work. I have to admit that although I have been discussing and evangelizing open science for over two years I have done very little of it. I have used this blog sometimes to put up small analysis or mini-reviews but never to describe ongoing projects. I have tried to start a side-project online but I over-es... Public Rambling blogs http://www.medworm.com/rss/comments.php?id=1955175 Wed, 12 Nov 2008 23:46:00 +0100 1955175 http://feeds.feedburner.com/~r/pedrobeltrao/~3/390877230/books-long-tails-and-crowds.html I read two interesting books recently that relate to how the internet is changing businesses and society in general.“The Long Tail” by Chris Anderson ends up suffering from its own success. I was so exposed to the long tail meme before reading the book that there were very few novel ideas left to read. The book describes the business opportunities that come from having a near-unlimited shelf space. While physical stores are forced to focus on the big hits, long tail businesses sell those big hits but also all the other niche products that only a few people will be interested in. There is a big challenge in trying to guide the users to those niche products that they will be interested. Anderson provides examples of recommendation and reputation engines from several companies (ie. Amazon... Public Rambling blogs http://www.medworm.com/rss/comments.php?id=1788657 Tue, 02 Sep 2008 14:05:00 +0100 1788657 http://feeds.feedburner.com/~r/pedrobeltrao/~3/363301670/freebase-parallax.html is a new browsing interface for Freebase. It allows the user to drill in and connect sets of objects to other sets of objects within Freebase and draw maps and graphs with the information. This really shows the power of having well structured data available online. Here is a video describing how it works with great examples of data mining: (Source: Public Rambling) Public Rambling blogs http://www.medworm.com/rss/comments.php?id=1700613 Tue, 12 Aug 2008 21:13:00 +0100 1700613 http://feeds.feedburner.com/~r/pedrobeltrao/~3/361811263/post-publication-journals.html With the increase in the number of journals and articles being published every year and the possibility of having an even larger set of "gray literature" available online we face the challenge of filtering out those bits of information that are relevant for us.Let us define as "perceived impact" this subjective measure of importance that some bit of information holds for us as scientists. This information is typically an article but it could be applied later to pre-prints and database entries in general.Everyone of us creates some rules to select from the constant stream of scientific output what to pay attention to. We could picture this sorting process in the form a triangle with a large base of very specific knowledge that is somewhat important to us and a small amount of more general b... Public Rambling blogs http://www.medworm.com/rss/comments.php?id=1696085 Sun, 10 Aug 2008 22:20:00 +0100 1696085 http://feeds.feedburner.com/~r/pedrobeltrao/~3/359991134/biobarcamp-wrapup.html In the last two days I attended the first BioBarCamp here in the bay area in the Institute for the Future. There is a lot of micro blogging coverage of the event in FriendFeed and even some recorded video from Cameron Neylon (click on demand and pick BioBarCamp).The meeting was fun due of the unstructured nature of the event and also because I got to meet a lot of people I knew only from blogs. Two highlights of the event were the talks by Aubrey de Grey (see notes and also Cameron's video above) and Jon Trowbridg from Google that talked about this.There were four parallel discussions going on but I kept mostly with the open science and web tolls related talks. There are a couple of ideas that I take away from these discussions that I will mention below but in general these overlap with wh... Public Rambling blogs http://www.medworm.com/rss/comments.php?id=1692107 Sat, 09 Aug 2008 01:27:00 +0100 1692107 http://feeds.feedburner.com/~r/pedrobeltrao/~3/347749174/some-backlash-on-open-science.html During ISMB, thanks to Shirley Wu (FF announcement), there was an improvised BoF (Birds of a Feather) session on web tools for scientists. Given that the meeting was not really announced we were not really expecting a full room. I would say that we had around 20 to 30 people that sayed at least for a while. We talked in general about tools that are useful in science (things like online reference managers, pre-print archives, community wikis, FriendFeed, Second Life) and we also talked a bit about the culture of sharing and open science.Curiosly, the most interesting discussion I had about open science was not at this BoF session but after it. In the following day the subject come up again in a conversation between me and tree other people (two PhD students and a PI from a different lab). I... Public Rambling blogs http://www.medworm.com/rss/comments.php?id=1658102 Sun, 27 Jul 2008 20:03:00 +0100 1658102 http://feeds.feedburner.com/~r/pedrobeltrao/~3/337664622/ismb-2008.html I am leaving soon to Toronto to attend ISMB 2008. I usually stay way from big conferences since typically in small conferences is easier to really have time to talk to everyone. The nice thing about attending a big conference is that it looks like everyone is there. There is no shortage of science bloggers attending and it is going to be nice to get to know the people behind some of the blogs for the first time.There is a room in FriendFeed were several people attending are gathered and for those not going it will probably be a good place to check for coverage of the conference. Alternatively here is a list of bloggers that are attending ISMB or some of the conferences before/after it:Adam KrautMichael KuhnDaniel JurczakNeil Saunders SouravRoland KrauseShirley WuJason StajichRuchira S. Dat... Public Rambling blogs http://www.medworm.com/rss/comments.php?id=1630956 Thu, 17 Jul 2008 02:21:00 +0100 1630956 http://feeds.feedburner.com/~r/pedrobeltrao/~3/327681867/on-plos-business-model.html Declan Butler wrote a news article about PLoS' business model that has generates a lot of discussion. A good summary of blog reactions is available from Bora's blog and there is a long thread of discussions at FriendFeed.It is hard to read the piece as impartial reporting due to the general negative undertone. Describing PLoS ONE as a database and referring to PLoS ONE and other PLoS journals of lower impact as "bulk, cheap publishing of lower quality papers". I have nothing against the factual content in the news piece. From that perspective it is an interesting report on the PLoS business model. According to the news story PLoS is on track to become economically self-sustainable within two years. We learn that this is possible due to the expansion of PLoS as a publisher to cover a broade... Public Rambling blogs http://www.medworm.com/rss/comments.php?id=1581883 Sat, 05 Jul 2008 21:45:00 +0100 1581883 http://feeds.feedburner.com/~r/pedrobeltrao/~3/324281806/bioinformatics-around-globe.html Did you ever wanted to have a global impression of the field of bioinformatics ? What types of tools they used, or how different is the work in academia versus industry ? Michael Barton from Bioinformatics Zen created a survey that will be running for the next month (until the 1st of August) that tries to address some of these questions. The more people complete the survey, the more informative the picture will be. The survey is anonymous and all information will be made available for those interested in analyzing it.If you have a blog you can re-post it on your blog (see intructions here) or send a link to any of these blog pages that host the survey to other bioinformatic/computational biology researchers. Loading... (Source: Public Rambling) Public Rambling blogs http://www.medworm.com/rss/comments.php?id=1560701 Tue, 01 Jul 2008 18:47:00 +0100 1560701 http://feeds.feedburner.com/~r/pedrobeltrao/~3/322757364/capturing-biology-one-model-at-time.html Mathematical and computational modeling is (I hope) a well accepted requirement in biology. These tools allow us to formalize and study systems of higher complexity that are hard to conceptualize with logic thinking. There have been great advances in our capacity to model different biological systems, from single components to cellular functions and tissues. Many of these efforts have been ongoing separately, each one dealing with a particular layer of abstraction (atoms, interactions, cells, etc) and some of them are now reaching a level of accuracy that rivals some experimental methods. I will try to summarize, in a series of blog posts, the main advances behind some of these models and examples of integration between them with particular emphasis on proteins and cellular networks. I inv... Public Rambling blogs http://www.medworm.com/rss/comments.php?id=1554379 Sat, 28 Jun 2008 21:37:00 +0100 1554379 http://feeds.feedburner.com/~r/pedrobeltrao/~3/311631697/world.html (caution, fiction ahead)I wake up in the middle of the night startled by some noise. Pulse racing I try to focus my attention outwards. Something breaking, glass shattering? Is someone out there ? I reach out with my senses but an awkward feeling nags at me, bubbling up to my consciousness. I try hard to focus, it is coming from outside the room , someone is inside my house. I close my eyes but vertigo takes over and weightlessness empowers me. I am in the living room cleaning the floor, picking up a broken glass. The nagging feeling finally assaults me fully. I am moving but I am not in control. Panic rises quickly as I watch helpless the simple and quiet actions of someone else. I stop picking up glass and I feel curious, only it is not exactly me, the feeling is there besides me.- Hi, w... Public Rambling blogs http://www.medworm.com/rss/comments.php?id=1518640 Thu, 12 Jun 2008 18:33:00 +0100 1518640 http://feeds.feedburner.com/~r/pedrobeltrao/~3/308493512/why-does-friendfeed-work.html I have been using FriendFeed for a while and I have to say that it works surprisingly well. It is hard to define what FriendFeed is so the only real way of understanding it is to try it for a while.One common way to define FF would be as a life-stream aggregator. Each user defines a set of feeds (blog, Flickr, Twitter, bookmarks, comments, etc) providing all other users with a single view of all the online activities of that user. Anyone can select how much to share (even nothing at all) and subscribe to a number of other users. Each item (photo, blog post, bookmark) can serve then as spark for discussions. The users can mark items as interesting or comment on them and this propagates to all other people that subscribe to you. In addition we can select sources to hide if for some reason th... Public Rambling blogs http://www.medworm.com/rss/comments.php?id=1508184 Tue, 10 Jun 2008 01:01:00 +0100 1508184 http://feeds.feedburner.com/~r/pedrobeltrao/~3/308312191/evaluation-metrics-and-pubmed-faceoff.html I have been reading recently a lot about evaluation metrics for papers and authors. It started with a blog post in Action Potential (Nature Neuroscience's blog) showing a correlation between the number of downloads of a paper and its citations. From the comments in that blog post I found out about a forum in Nature Network about Citation in Science and also the recently published group of perspectives on "The use and misuse of bibliometric indices in evaluating scholarly performance".It could have been a coincidence but Pierre sparked a long discussion in FriendFeed when he suggested it would be nice to be able to sort Pubmed queries by the imapact factor of the journal. In reaction to this Euan set up a very creative interface to Pubmed that he named Pubmed Faceoff. He took several differ... Public Rambling blogs http://www.medworm.com/rss/comments.php?id=1502486 Mon, 09 Jun 2008 20:35:00 +0100 1502486 http://feeds.feedburner.com/~r/pedrobeltrao/~3/290368291/prediction-of-phospho-proteins-from.html I want to be able to predict what proteins in a proteome are more likely to be regulated by phosphorylation and hopefully use mostly sequence information. This post is a quick note to show what I have tried and maybe get some feedback from people that might have tried this before.The most straightforward way to predict the phospho-proteins is to use existing phospho-site predictors in some way. I have used the GPS 2.0 predictor on the S. cerevisiea proteome with medium cutoff and including only Serine/Threonine kinases. The fraction of tyrosine phosphosites in S. cerevisiae is very low so I decided to for now not try to predict tyrosine phosphorylation.This produces a ranked list of 4E6 putative phosphosites for the roughly 6000 proteins scored according to the predictor (each site is scor... Public Rambling blogs http://www.medworm.com/rss/comments.php?id=1442731 Wed, 14 May 2008 00:26:00 +0100 1442731 http://feeds.feedburner.com/~r/pedrobeltrao/~3/285717695/drug-drug-interactions-and-network.html How does the effect of drug-drug combinations relate to the cellular interactions of their targets ? Last year, Joseph Lehár and colleagues published a paper in MSB looking into this question.One way to study the effect of drug combinations on growth of a bacteria for example is to measure the inhibition of growth of all possible combinations of serially diluted doses of two combined drugs and plotting dose-matrices like the ones shown in figure 1 of the paper and shown here adapted from the paper. In fig1A the authors show how the combined effect of increasing doses of two drugs inhibit the growth of a methicillin-resistant Staphylococcus aureus strain. Light colors are equivalent to a strong inhibition of drug. One observation from this figure is that the two drugs can inhibit the growt... Public Rambling blogs http://www.medworm.com/rss/comments.php?id=1428941 Wed, 07 May 2008 22:01:00 +0100 1428941 http://feeds.feedburner.com/~r/pedrobeltrao/~3/277231935/scifoo-and-biobarcamp.html (Via Attila) The invitations for the 3rd SciFoo have apparently been sent. It will be held from the 8th to the 10th of August at the Googleplex. There is also an idea floating around to organize a BarCamp at the same time as SciFoo. A BarCamp Check out the BioBarCamp wiki and discussion group. There are already several suggestions for venues to organize it and several people interested in attending.On a side note it's fun to see something like this getting thought of and set up from Twitter/FriendFeed conversations. I have been trying out FriendFeed for a while now and although I am not a big fan of micro blogging (yet?) I really like the conversations around the feed streams. (Source: Public Rambling) Public Rambling blogs http://www.medworm.com/rss/comments.php?id=1397599 Thu, 24 Apr 2008 22:39:00 +0100 1397599 http://feeds.feedburner.com/~r/pedrobeltrao/~3/271808248/shuffle-project.html Most of my work in the last few years was computational, either looking at the evolution of protein-protein interactions or at the prediction of domain-peptide interactions. The nice thing of working on a lab were a lot of people were doing wet lab experiments was that I had the oportunity to, once in a while, grab some pipettes and participate in some of the work that was going on. One project that worked out well was published today (not open access sorry). My contribution to this project was small but it was a lot of fun and I am very interested in the topic that we worked on. We called it the shuffle project in lab. The main objective of this work was to study how the addition of gene regulatory interactions impacts on a cell's fitness. We introduced different combinations of existing ... Public Rambling blogs http://www.medworm.com/rss/comments.php?id=1377926 Wed, 16 Apr 2008 22:56:00 +0100 1377926 http://feeds.feedburner.com/~r/pedrobeltrao/~3/270154245/life-sciences-virtual-conference-and.html IBM Deep Computing will hold a 2 day virtual conference on Innovations in Drug Discovery and Development (16th and 17th of April 2008). The talks will be recorded and available for playback for those that register. The focus of the talks will be on the impact of High Performance Computing for life science research. The current list of talks: Dr. Paul Matsudaira, Director Whitehead Institute Professor of Biology and Bioengineering, MIT : Advanced Imaging and Informatics Methods for Complex Life Sciences Problems Professor Jan-Eric Litton, Director of Informatics, Karolinska Institute - Biobanking : The Challenge of Infrastructure for Large Scale Population StudiesDr. Joel Saltz, Professor and Chair, Department of BioMedical Informatics, Ohio State University : The Cancer Biomedical Inform... Public Rambling blogs http://www.medworm.com/rss/comments.php?id=1370709 Mon, 14 Apr 2008 17:35:00 +0100 1370709 http://feeds.feedburner.com/~r/pedrobeltrao/~3/266602032/structure-based-prediction-of-sh2.html One of the last few things I worked on during the PhD is now available in PLoS Comp Bio. It is about the structure based prediction of binding of SH2 domains to phospho-peptide targets. The SH2 domain (src homology domain 2) is a small domain of around 100 amino-acid that has a strong preference to bind peptides that have phosphorylated tyrosines. The selectivity of each domain is typically further restricted by variable surfaces near the phospho-tyrosine binding pocket. See figure below:The binding preference of each domain can be experimentally determined using for example peptide library screening, phage display or protein arrays. Alternatively we should be able to analyze the increasing amount of structural information and predict the binding specificity of peptide binding domains. We ... Public Rambling blogs http://www.medworm.com/rss/comments.php?id=1358504 Tue, 08 Apr 2008 20:17:00 +0100 1358504 http://feeds.feedburner.com/~r/pedrobeltrao/~3/266576401/bioblogs20-very-late-edition.html I said I would organize the 20th edition of Bio::Blogs here on the 1st of April but April fools and my current work load did not allow me to get Bio::Blogs up on time. There were a couple of interesting discussions and blog posts in March worth noting. For example, Neil mentioned a post by Jennifer Rohn started that initiated what could be one of the longest threads in Nature Network :"In which I utterly fail to conceptualize". It started off as small anti-Excel rant but turned in the comments to 1st) a discussion of bioinformatic tools to use, 2nd) a discussion of wet versus dry mindset and how much one should devote to learn the other. Finally it ended up as a exchange about collaborations and how a social networking site like Nature Network could/should help scientists find collaborator... Public Rambling blogs http://www.medworm.com/rss/comments.php?id=1358505 Tue, 08 Apr 2008 17:11:00 +0100 1358505 http://feeds.feedburner.com/~r/pedrobeltrao/~3/262215058/leveling-playing-field-nih-to-ban-brain.html There has been quite a buildup of discussion surrounding the idea of brain enhancing drugs in the last couple of days. It started early march with a New York Time piece “Brain Enhancement Is Wrong, Right?” and it has culminated with the recent announcement of the World Anti Brain Doping Authority (WABDA) a joint effort from the NIH and EU to initiates studies on the reach of brain enhancing practices in science today. There are many points of view already expressed on the web, see for example: · Chris Patil· Bora· Anna Kushnir· Genome Technology· Sunclipse· Egghead· Eye on DNA· Bob Ohara· Martin Fenner· Jennomics My first reaction was of pure skepticism, this must be some kind of joke I thought, so I tried to probe a little bit around the UCSF campus to see if anyon... Public Rambling blogs http://www.medworm.com/rss/comments.php?id=1344150 Tue, 01 Apr 2008 20:58:00 +0100 1344150 http://feeds.feedburner.com/~r/pedrobeltrao/~3/261600145/call-for-bioblogs-20.html The 20th edition of Bio::Blogs will be posted here by the end of tomorrow. This is very short notice but if anyone would like to contribute please send a few links of the most interesting things of the past month and I will put everything together (email bioblogs at gmail). (Source: Public Rambling) Public Rambling blogs http://www.medworm.com/rss/comments.php?id=1340501 Mon, 31 Mar 2008 23:42:00 +0100 1340501 http://feeds.feedburner.com/~r/pedrobeltrao/~3/255734174/structured-abstract-experiment-at-febs.html The journal "FEBS letters" is starting a publishing experiment on structured abstracts. As described in the editorial the experiment is aimed at:"integrating each manuscript with a structured summary precisely reporting, with database identifiers and predefined controlled vocabularies, the protein interactions reported in the manuscript."The experiment will be a collaboration between FEBS letters and the interaction database MINT, it has started in the beginning of this year and it will last 6 months. It will try to evaluate the necessary tools and the authors's "degree of interest (and competence) to invest" in this annotation process. It will be very interesting to see the results of this experiment to see if authors are willing to do this extra bit of work and how much this might facili... Public Rambling blogs http://www.medworm.com/rss/comments.php?id=1320513 Fri, 21 Mar 2008 20:42:00 +0100 1320513 http://feeds.feedburner.com/~r/pedrobeltrao/~3/247816885/bioblogs-19-bioengineering.html This months edition of Bio::Blogs is now available at Duncan's blog and it is mostly focused on (bio)engineering. Click the link for a summary of interesting things that were blogged about in the past month. I will be hosting issue number 20 here in the blog, without a clear topic. Possibly with some emphasis on data integration. Email your top picks of the month until the end of March to bioblogs at gmail .com (Source: Public Rambling) Public Rambling blogs http://www.medworm.com/rss/comments.php?id=1287789 Sat, 08 Mar 2008 07:35:00 +0100 1287789 http://feeds.feedburner.com/~r/pedrobeltrao/~3/244552515/design-mutate-and-freze.html Drew Endy talked about engineering biology for Edge. Most of the emphasis is still on standardization of biological parts and the importance of simplifying the process of creating a biological function. Still it would be nice to hear from him some new ideas about establishing processes of engineering biology. His whole speech seems focused on creating the hacker culture in biology. To transpose all the same concepts that would allow us to re-create the explosive growth of tinkering and production that we saw for electronics and computer programing within the biological sciences.I agree with most of what he says, that we should: 1)focus on method development; 2)work on a registry of parts and 3) foster an "open source"/hacker culture in synthetic biology. In this text he did not mention for... Public Rambling blogs http://www.medworm.com/rss/comments.php?id=1272494 Sun, 02 Mar 2008 23:29:00 +0100 1272494 http://feeds.feedburner.com/~r/pedrobeltrao/~3/241355221/jonathan-eisenplos.html PLoS has a new Academic Editor in Chief that blogs, works on evolution and has been at SciFoo twice. Jonathan A. Eisen, explains his reasons for accepting the job in an editorial available online. Among other things, he states:Second, I want to work with the professional staff at PLoS Biology, the Academic Editors, and anyone else in the community who shares my desire to build new initiatives that will keep PLoS Biology as a top-tier journal. These would include ideas like producing issues dedicated to particular themes, actively recruiting excellent papers in fields where OA is not yet common, producing more outreach and educational material, and engaging bloggers and fully embracing the Web 2.0 world.I actually would like to get a bit more involved with what they are doing at PLoS, in p... Public Rambling blogs http://www.medworm.com/rss/comments.php?id=1256193 Tue, 26 Feb 2008 07:25:00 +0100 1256193 http://feeds.feedburner.com/~r/pedrobeltrao/~3/239542755/call-for-bioblogs19.html Duncan Hull has volunteer to host the next issue of Bio::Blogs (a bioinformatic related monthly blog journal). It will be out in the beginning of March on the O'Really? blog. The suggested theme for this month is the relationship between Biology and Engineering inspired on the interview published on Edge.org "Engineering and Biology": A Talk with Drew Endy. Anyone can send links for this issue on this topic but also for other interesting bioinformatic posts to bioblogs at gmail.comWe could also try to format if automatically using FeedJournal as suggested by Neil. (Source: Public Rambling) Public Rambling blogs http://www.medworm.com/rss/comments.php?id=1250124 Fri, 22 Feb 2008 18:01:00 +0100 1250124 http://feeds.feedburner.com/~r/pedrobeltrao/~3/236736070/late-links-bioblogs18-new-blog.html I have been away from the web for the last few weeks as I moved to San Francisco to start my first postdoc. I will be working at UCSF in the Lim Lab and the Krogan lab on the evolution of signaling in yeasts. I'll try to blog more about it later during the year. I am looking forward to getting to know the bay area and hopefully make the most of the great (and apparently relaxed) science & technology environment.Early this month Michael Barton edited another great edition of Bio::Blogs mostly dedicated to open science. He also put together an essay on the subject that is worth reading and commenting on. The next edition of Bio::Blogs will probably come back here to Public Rambling on the 1st of March (unless there is another volunteer).Also in these last few weeks Lars Juhl Jensen start... Public Rambling blogs http://www.medworm.com/rss/comments.php?id=1238128 Fri, 08 Feb 2008 20:32:00 +0100 1238128 http://feeds.feedburner.com/~r/pedrobeltrao/~3/223432422/submissions-for-bioblogs18.html I am slowly re-connecting to the online world again, trying to pick trough the thousands of blog posts and other RSS feed alerts piled up in GReader. Way before I manage to do that (unless I press the read all button) the next edition of Bio::Blogs will be up at Bioinformatics Zen. Michael Barton has kindly agree to host the 18th edition of Bio::Blogs with a particular emphasis on Open Science and Open Notebook Science. It is scheduled for February 1st and anyone can participate by sending a link of their submissions to bioblogs at gmail.com.To get in the spirit of the upcoming edition and to inspire some related blog posts go check out his recent movie. What do you think ? Will there be a significant increase of people sharing and collaborating online this year ? (Source: Public Rambling) Public Rambling blogs http://www.medworm.com/rss/comments.php?id=1179633 Sat, 26 Jan 2008 10:27:00 +0100 1179633 http://feeds.feedburner.com/~r/pedrobeltrao/~3/205196151/disconnecting-for-while.html Image credit: Duff SudsI am disconnecting from blogging for longer than usual. There will not be a Bio::Blogs edition on the 1st of January but there will be one dedicated to Open Science on the 1st of February. Before I go, congratulation to the chemioinformatics related blogging group that got a paper from combined efforts. Also, have a look at the new blog from Jason Kelly called Free Genes that will focus on synthetic biology and open science issues.I'll be back sometime in the end of January. Happy celebrations to everyone and a good start to the new year. (Source: Public Rambling) Public Rambling blogs http://www.medworm.com/rss/comments.php?id=1113870 Sun, 23 Dec 2007 16:58:00 +0100 1113870 http://feeds.feedburner.com/~r/pedrobeltrao/~3/195280135/open-science-project-on-domain-family.html Some domain families of similar function have expanded more than others during evolution. Different domain families might have significantly different constraints imposed by their fold that could explain these differences. This project aims to understand what properties determine these differences focusing in particular on peptide binding domains. Examples of constraints to explore include average cost of production or capacity to generate binding diversity for the domain family. This project is also a test for using Google Code as a research project management system for open science (see here for project home). Wiki pages will be used to collect previous research and milestone discoveries during the project development and to write the final manuscript towards the end of the project. Iss... Public Rambling blogs http://www.medworm.com/rss/comments.php?id=1070976 Wed, 05 Dec 2007 01:22:00 +0100 1070976 http://feeds.feedburner.com/~r/pedrobeltrao/~3/193911559/merry-bioblogs-everyone.html Paulo Nuin hosted the 17th edition of Bio::Blogs. The number of submissions was very low so I suspect I am not the only one rushing to finish everything before going on holidays. Should we skip the edition of the 1st of January or maybe postpone it for a few days ? Anyone interested in hosting ? I have been thinking of changing the format a little bit to try to increase the incentives for participating but I'll leave this for another post. (Source: Public Rambling) Public Rambling blogs http://www.medworm.com/rss/comments.php?id=1064824 Sun, 02 Dec 2007 15:18:00 +0100 1064824 http://feeds.feedburner.com/~r/pedrobeltrao/~3/191421191/bioblogs-17-call-for-submissions.html The 17th edition of Bio::Blogs will be hosted by Paulo Nuin at Blind.Scientist . Submissions of interesting bioinformatic related blog posts of this month can be sent, until the end of the November, to the usual address (bioblogs at gmail dot com) or to nuin at genedrift dot org. There is also still time to submit blog posts to the OpenLab 2007 compilation. (Source: Public Rambling) Public Rambling blogs http://www.medworm.com/rss/comments.php?id=1054766 Tue, 27 Nov 2007 18:41:00 +0100 1054766 http://feeds.feedburner.com/~r/pedrobeltrao/~3/187308161/linking-out-open-science-and-new-blog.html Cameron Neylon posted a request for collaboration in his blog:...we are using the S. aureus Sortase enzyme to attach a range of molecules to proteins. We have found that this provides a clean, easy, and most importantly general method for attaching things to proteins.(...)We are confident that it is possible to get reasonable yields of these conjugates and that the method is robust and easy to apply. This is an exciting result with some potentially exciting applications. However to publish we need to generate some data on applications of these conjugates.They are looking for collaborators interested in applying this method. Go check the blog posts if you are interested or know someone that works on something similar. (via Open Access News) Liz Lyon, Associate Director of UK Digital Curatio... Public Rambling blogs http://www.medworm.com/rss/comments.php?id=1036849 Mon, 19 Nov 2007 18:54:00 +0100 1036849 http://feeds.feedburner.com/~r/pedrobeltrao/~3/187284392/linking-out-personalized-medicine.html Personalized medicine continues to climb the hype cycle. I have been getting most of the best news coverage on the subject from blogs.- Bertalan Meskó reviews companies focused on personalized medicine (see part I and II)- Attila Csordas and Deepak Singh cover the social aspects of personal health and the tie-in to 23andMe- Gareth Palidwor reads into the details to speculate that the business model of 23andMe might be to sell the aggregated user data.- Gene Sherpas puts on the brakes, describing the hype as Genomic VoyeurismI am concerned that all the attention the genomics side of personalized medicine will distort the relative importance of nature versus nurture. Everyone craves for a peek at their own destiny and at their roots. These services hope to provide both of these by looking a... Public Rambling blogs http://www.medworm.com/rss/comments.php?id=1036850 Mon, 19 Nov 2007 16:49:00 +0100 1036850 http://feeds.feedburner.com/~r/pedrobeltrao/~3/184111494/last-call-for-open-laboratory-2007.html Bora has issued a last call for submissions to the Science Blogging anthology of 2007. As last year, the objective is to collect some of the best science blog posts of the year and compile it into a book to print on demand (deadline on December 20th 2007). Submissions can be sent using an online form and they will be reviewed by a panel that will compile the final list.Anyone interested in participating can send in links to their favorite blog posts of the year and also volunteer to be part of the reviewing process (see instructions here). (Source: Public Rambling) Public Rambling blogs http://www.medworm.com/rss/comments.php?id=1022131 Tue, 13 Nov 2007 13:08:00 +0100 1022131 http://feeds.feedburner.com/~r/pedrobeltrao/~3/183633526/4th-year-blog-anniversary.html It is hard to believe that is has been 4 years that I started blogging here. Not that I am a very prolific blogger with only 328 blog posts in this time. These are not very evenly distributed with more than 200 blog posts in the last two years. The style of blog posts also changed a lot from a link blog with a few sentences to longer more opinionated posts.Having a glance a the blog posts it is easy to find some very weird ones :)Your Identity Aura (2005)Our Collective Mind (2005)The Human Puppet (2005)Social Network Dynamics in a Conference Setting (2006)The Fortune Cookie Genome (2007)There a lot of serious ones too but I will leave that list to some other time.Thanks to Nodalpoint and the Nodalpoint regulars (Greg, Neil, Alf and Chris) for introducing me to blogging some 6 years ago and... Public Rambling blogs http://www.medworm.com/rss/comments.php?id=1021222 Mon, 12 Nov 2007 14:54:00 +0100 1021222 http://feeds.feedburner.com/~r/pedrobeltrao/~3/182884781/predicting-functional-association-using.html About a month ago Lécuyer and colleagues published a paper in Cell describing an extensive study of mRNA localization in Drosophila embryos during development. The main conclusion of this study was that a very large fraction (71%) of the genes they analyzed (2314) had localization patterns during some stage of the embryonic development. This includes both embryonic localization or sub-cellular localizations.There is a lot of information that was gathered in this analysis and it should serve as resource for further studies. There is information for different developmental stages so it should also be possible to look for the dynamics of localization of the mRNAs. Another application of this data would be to use it as information source to predict functional association between genes.Protein... Public Rambling blogs http://www.medworm.com/rss/comments.php?id=1018796 Sat, 10 Nov 2007 21:04:00 +0100 1018796 http://feeds.feedburner.com/~r/pedrobeltrao/~3/181685661/what-i-dont-like-about-bpr3.html For those that have not heard about it before BPR3 stands for Bloggers for Peer-Reviewed Research Reporting. From their website:"Bloggers for Peer-Reviewed Research Reporting strives to identify serious academic blog posts about peer-reviewed research by offering an icon and an aggregation site where others can look to find the best academic blogging on the Net."It is all great except that it already exists and for a long time before BPR3. You can go to the papers section in Postgenomic and select papers by the date they were published, were blogged about, how many bloggers mentioned the paper or limit this search to a particular journal. I have even used this early this year to suggest that the number of citations increases with the number of blog posts mentioning the paper. In this case ... Public Rambling blogs http://www.medworm.com/rss/comments.php?id=1014897 Thu, 08 Nov 2007 14:40:00 +0100 1014897 http://feeds.feedburner.com/~r/pedrobeltrao/~3/178258440/right-to-equivalent-response.html (disclaimer: I worked for Molecular Systems Biology) The last issue of PLoS Biology caries an editorial about Open Access written by Catriona J. MacCallum. It addresses the definition of Open Access and what the author considers an "insidious" trend of obscuring "the true meaning of open access by confusing it with free access". I agree with the main point of the editorial, that we should keep in mind the definition of open access and that the capacity to re-use a published work should have more value to the readers. However, it is very unfortunate that the very fist example MacCallum picks on is the Molecular Systems Biology journal for the simple fact that very recently they have changed the publishing policies to address exactly this issue. Authors can choose one of two CC licenses, dec... Public Rambling blogs http://www.medworm.com/rss/comments.php?id=998569 Thu, 01 Nov 2007 13:47:00 +0100 998569 http://feeds.feedburner.com/~r/pedrobeltrao/~3/178234183/bioblogs-16-one-with-halloween-theme.html The 16# edition of Bio::Blogs is know available at Freelancing science. Jump over there for summary of what has been going on during this month in the bioinformatic related blogs. If not for anything else then just to have a look at the pumpkin. Thanks again to everyone that participated. Paulo Nuin from Blind.Scientist has volunteered to host the 17# edition that is scheduled to appear as usual on the 1st of December. (Source: Public Rambling) Public Rambling blogs http://www.medworm.com/rss/comments.php?id=998570 Thu, 01 Nov 2007 13:21:00 +0100 998570 http://feeds.feedburner.com/~r/pedrobeltrao/~3/174936395/building-e-science-platform-with.html (via Frank Gibson's Peanutbutter) Hugo Hiden, the technical director of the North-East Regional e-Science Centre (NEReSC) started a new blog where he will explore how to build an e-Science platform based on Microsoft technology. The initial post explains a little bit why he is doing this:"The reason for this blog is, primarily, to document my experiences with writing a prototype e-Science research platform using Microsoft tools instead of the more traditional approach of fighting with Open Source. This way is easier, supposedly."and also, what he aims to build:"The task I have set myself is to recreate, at a basic level, the software being developed by the CARMEN project (http://www.carmen.org.uk). "Let's see how it goes. Maybe they'll take suggestions later on :). (Source: Public Rambling... Public Rambling blogs http://www.medworm.com/rss/comments.php?id=979126 Thu, 25 Oct 2007 16:49:00 +0100 979126 http://feeds.feedburner.com/~r/pedrobeltrao/~3/172908514/bioblogs-16-call-for-submissions.html The next edition of Bio::Blogs (bioinformatics blog journal) will be hosted at Freelancing science on the 1st of November. If you find anything this month that you think is interesting to add to this addition send an email to bioblogs at gmail. com until the end of the month. Anyone interested in hosting future edition can also send an email to volunteer. (Source: Public Rambling) Public Rambling blogs http://www.medworm.com/rss/comments.php?id=966877 Sun, 21 Oct 2007 14:35:00 +0100 966877 http://feeds.feedburner.com/~r/pedrobeltrao/~3/172206114/fortune-cookie-genome.html *in an imaginary future*Today is the day I get the sequencing results back. It is going be interesting to have finally a glimpse of my very own genome. At the same time I am afraid of the potential disease associations they might find in there. In any case I rather know it with time to do something about it. Thats it ... I exhale and open the main door to the building walking up the desk.- Hi. I have an appointment with my genetic adviser.- Oh yes, go up to the 3rd floor, they are expecting you.I walk up a DNA shaped stairway and walk into the office of one of the attending specialists. He was the one convincing me of how useful it would be to purchase the GenomeSurvey(TM) package.- I got your email. The results are in ?- Yes, we have your genome fully sequenced and uploaded into your serv... Public Rambling blogs http://www.medworm.com/rss/comments.php?id=964519 Fri, 19 Oct 2007 16:21:00 +0100 964519 http://feeds.feedburner.com/~r/pedrobeltrao/~3/168232603/journalfire.html A new science related service called JournalFire has started. It was apparently created by a group of graduate students that are "frustrated with the current system of scientific discourse and publication". According to the initial blog post this service "provides a centralized location for you to share, discuss, and evaluate published journal articles. You, the scientists, are put in charge of determining what studies are significant and noteworthy."I did not have a chance to test it since it is in private beta but I have asked for an account. It looks like anyone with an .edu account should be able to access it already. It sounds promising but has many of these services a lot depends on the capacity to attract a sufficiently large group of people to sustain interesting discussions. I wil... Public Rambling blogs http://www.medworm.com/rss/comments.php?id=942956 Thu, 11 Oct 2007 02:27:00 +0100 942956 http://feeds.feedburner.com/~r/pedrobeltrao/~3/163958824/bioblogs-15.html Welcome to the 15th edition of the bioinformatics blog journal Bio::Blogs.I complained a while ago that there was very little expansion of the bioinformatics blogging community but at least in the last couple of months it looks like this is changing. Although not necessary started last month here are three blogs that I only recently noticed: At the end of the day from Stephen Spiro (Spiro lab homepage), Paradoxus and Saaien Tist from Jan Aerts.Not only are there more blogs there are many more examples of bloggers posting original ideas and research. Most people agree that being open about research should foster collaboration but so far few people have really tried to do it. It is inspiring to read trough these examples and trying to imagine how we might be doing science in the next couple ... Public Rambling blogs http://www.medworm.com/rss/comments.php?id=918852 Mon, 01 Oct 2007 22:04:00 +0100 918852 http://feeds.feedburner.com/~r/pedrobeltrao/~3/163802843/icsb-2007-i-am-attending-eighth.html I am attending the eighth International Conference on Systems Biology (ICSB 2007) in Long Beach. I typically prefer smaller conferences but this one is probably the best one to get an overview of the recent progress in systems biology. As expected the program has a broad scope and unlike last year's meeting there are no parallel sessions so I will have a chance to ear more from others fields. Any other bloggers attending ? (Source: Public Rambling) Public Rambling blogs http://www.medworm.com/rss/comments.php?id=917905 Mon, 01 Oct 2007 16:40:00 +0100 917905 http://feeds.feedburner.com/~r/pedrobeltrao/~3/143214990/ephemeral-journal-recently-i-mentioned.html The ephemeral journalRecently I mentioned the start of yet another journal covering one of the topics I would place on the top of a hype cycle curve. This together with the apparent ever increasing number of journals everywhere got me thinking of birth/death of science journals. The cost of starting up a new journal is so low that the turn-over can only be higher. Still, we don't typically see a lot of "journal death". They are meant to be respected and built up reputation among the public audience they serve. It looks however inevitable that with a limited attention capacity and ever increasing number of journals that science hype cycles might have a strong influence on a journals activities. If hyped up subjects sprout out new journals quickly (i.e stem cells, systems biology, synthetic ... Public Rambling blogs http://www.medworm.com/rss/comments.php?id=793911 Sat, 11 Aug 2007 23:40:00 +0100 793911 http://feeds.feedburner.com/~r/pedrobeltrao/~3/143100426/quotes-another-interesting-sciview.html QuotesAnother interesting SciView interview is available at Blind.Scientist. Here is one quote from Alexei Drummond (Chief Scientist of Biomatters) that I liked:"I think that bioinformatics has to become a field where people without programming skills can contribute substantially. I would argue that all of the programmers in bioinformatics should be working very hard to program themselves out of their jobs (and into more satisfying jobs)."Science advances quickly and so do the computational needs. Can we ever do away with these one off scripts if there are always new data types and innovative ways of analyzing them ? I guess the ideas around workflows and such could lead to very visual oriented programing that anyone can do. (Source: Public Rambling) Public Rambling blogs http://www.medworm.com/rss/comments.php?id=793674 Sat, 11 Aug 2007 15:22:00 +0100 793674 http://feeds.feedburner.com/~r/pedrobeltrao/~3/142415478/first-issue-of-iet-synthetic-biology.html First issue of IET Synthetic BiologyThe first issue of (yet) another journal related to systems&synthetic biology is now online. IET Synthetic Biology will be freely available during this year. This issue covers several works from iGEM and the editorial is worth a read to have a look at the future direction of the journal.In addition to conventional research and review articles, we see an important need for practical articles describing technical advances and innovative methods useful in synthetic biology. We will encourage submission of technical articles that might describe novel BioBrick components, construction techniques, characterisation of a new biological circuit, new software or a practical ‘hands-on’ guide to the construction of new instrumentation or a biological device.In a... Public Rambling blogs http://www.medworm.com/rss/comments.php?id=790512 Thu, 09 Aug 2007 10:54:00 +0100 790512