MedWorm.com provides a medical RSS filtering service. Over 5000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'The Omics world' source. Sat, 16 Aug 2008 14:48:13 +0100 http://harijay.wordpress.com/2008/06/06/my-attempts-at-explaining-personal-genomics/ The other day I was talking to my parents about the fascinating world of personal genomics and I ventured to write up my description of some of the ideas behind the hapmap and personal genomics in an email. I am reproducing the email here and hoping that I can get pointers on explaining things better ( I am after all only a biochemist/structural biologist)  The world of personal genomics is upon us. Companies like 23andMe and deCode will run your genetic sample against a known list of variation markers and tell you things about yourself as suggested by your genes. or they will tell you what markers you share with what groups of people. Although this sounds amazing , a lot of this is very nuanced and understanding it is a fun exercise. Also all of this will change evrything or atleast it has the potential to. Lets start at the begining , when you ask yourself to be “typed” or what do my genes have? What is this stuff all about We are all quite different, i.e you and me will probably have several hundreds of thousands of  differences between the two of us. To actually estimate exactly how different you and me are , this will require a full sequencing of our genomes . This is quite expensive and takes a lot of time .  Instead imagine if I told you that that scientists have figured out that these differences occur in groups i.e they are linked together. Very crudely..if one of these jumps from you to your child..it will take a few thousands of its neighbors along for the ride.  So now instead of getting information about the several hundred thousand actual differences , we can learn a lot by just looking at the tens of thousands of these labels . In each case for a particular label ( or marker or SNP) we can look at all the variation determined this far. i.e at position 59 all know human variation has either a A or a T. So you can belong to one of those two groups. Now, Once you get this or any such  label you can infer the rest that such a label is tied to. Collecting information on these labels is what projects like the hapmap do ( see hapmap.org) and it is exactly the identity of these labels that a genotyping service will provide you with ( for an example see http://www.snpedia.com/files/promethease/outputs/promethease-ngnomics.html).   SO whats the big deal? . All of science is trying to figure out, what makes a person A die of a heart-attack before he was 20 , while person B lives till he was 80. As well all know , there are two parts to this story “Nature : or your genes” and “Nurture - or your liefetsyle”. Science can easily attempt to understand your genes. Because that is “hard” information. And in the case of person A and B , science asks the question, whats in their genes that might have led to the outcome. So coming back to the point I made in the prevous few paras , instead of looking at the entire genome  for differences between person A and B , we can start by asking what markers or labels do they share and what do they not share. Then, taking the markers they dont share . Which among those are common with people who had heart-attacks early. So,  looking at this information may lead to some clues about which genes A or B had led to their resultant life-expectancies. Lets take another example , say you want to test in advance  “what genes cause allergies to Sulfur drugs ” . So what you would do is give many people sulfur drugs and then check all the people who were allergic and look at what groups their genes belong to. At the end of which you ask the obvious question..all those people who came up with severe allergies to sulfur , what group ( or markers ) did they have in common. In most cases this is not a single gene or single number  , but  for simplicity, the answer you get is something like : if you have group A59C (also known as single nucleotide polymorphism or SNP) then you have a 20% chance of being allergic . Also , since most traits dont depend on only one label or marker , the answers are quite diffused and are given in terms of probabilities. Say a 20% chance of A59C may be converted to a 80% chance in combination with label G456A and a 0.2 % chance if you had F555A . Do you get the point? If you dont dont worry as you can tell it is quite complicated! Regardless. The chances are that, the more we ask such questions , the more we learn about these probabilities and that  is what most genetic research is looking to do. So instead of studying say 10000 mostly white americans , things become more meaningful if you study 1000,000 people from every corner of this earth . Then the numbers may all add up and give us a more clear label to associate with any given outcome , like a heart-attack . Thats what the hapmap is all about. Anyways getting back to the point,  Such studies are what give rise to the field of  personal genomics i.e look at what markers you have and then compare them with known marker-result associations or known drug-effect associations. As I have already hopefuly convinced you : these studies are very nuanced. People expect  cut-and-dry answers and many may  return disappointed. Also people prone to hypochondria , should definitely stay away , lest that 2% chance that you will have a heart-attack will be converted to a very high percent chance of you getting it , actually because of the stress you put yourself through as a result of this knowledge ( the nurture  or lifestyle part). Also this points to how these studies if carried out correctly will  change a lot of things , medicine , health-care , the very nature of how we view ourselves. These studies can attempt to answer questions like how similar are south and north Indians genetically . And as I just told you , nature is not cut and dry and neither is human history!. So interpreting especially these results with social or political  implications is a double edged sword!  Before I end , you can check out one of these reports as is given by companies like 23andme . http://www.snpedia.com/files/promethease/outputs/promethease-ngnomics.html So are you excited? Do you want to find out whether you have a 10% chance of arthritis ? or a 40% chance that you have descended from a caucasian lineage? more Reading on this topic: http://www.hapmap.org/ For the medically inclined . You can read an article in science that talks about the implications of these studies for healthcare studies published in the science magazine (Source: The Omics world) The Omics world blogs http://www.medworm.com/rss/comments.php?id=1499946 Fri, 06 Jun 2008 21:54:51 +0100 1499946 http://harijay.wordpress.com/2007/10/15/under-the-hood-web-20-pubmed-and-rss/ Snap poll: Did you know that PUBMED and a lot of the NCBI gives you the ability to create custom RSS feed around just about any query My Answer : Yes I do ..but I learnt about this feature very recently, and I have been using PUBMED for years. You can watch how this feature works from this screencast . The reason I bring this up is my observation that the NCBI and the EBI have been putting in a lot of energy at staying current while  preserving their orginal interface. Under the hood at the NCBI you can find features like MY-NCBI which has some killer personalization options ( to borrow a web 2.0 buzzword) . The NCBI forms have started to use more and more javascript and things  have started to look “more ajaxy” . Even the collections option just about ensures that I dont use connotea as often ( other than when I want to share collections on the web). The point is that the bio-search space has and continues to see variations to the theme of search. A lot of these offerings seem to be mere duplications of functionality already present at the EBI and NCBI. While this is a good thing and only through such attempts will we arrive at a “Google”( in the verb sense) for biosearch. I sometimes wonder if it would just be more worthwhile for atleast the career scientists among us, to learn how to use NCBI and EBI first. Then maybe private research dollars could be diverted to tackle the harder problems in bio-search . References: Helia seraches PUBMED/MEDLINE (Source: The Omics world) The Omics world blogs http://www.medworm.com/rss/comments.php?id=952122 Mon, 15 Oct 2007 14:09:13 +0100 952122 http://harijay.wordpress.com/2007/10/06/i-feel-chicken-gunya-can-social-networks-help-track-emerging-diseases/ 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 better. While the debate on the best way to handle health information online continues, I was wondering how open I would be to sharing information about what afflicts me, if there was a societal benefit to be derived from it. It could something as simple as monitoring allergy symptoms around where I live or something fancy like tracking an emerging pathogen. Imagine all of us updating a common channel with “de-personalized” information on what afflicts us globally.   I can imagine the system to be something like this ..I  could “submit” to this service information about what ails me ..and the machine could obfuscate my details , preserving only things like my approximate geographical area and my age and sex and add it to this health information social network. If implemented well could  possibly then have daily visualizations along the lines of  “We feel fine” to possibly something like  “We feel chicken Gunya” (Source: The Omics world) The Omics world blogs http://www.medworm.com/rss/comments.php?id=932042 Sat, 06 Oct 2007 06:57:54 +0100 932042 http://harijay.wordpress.com/2007/10/04/of-6-web-hosts-and-dying-web-apps/ 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 and other immunological proteins from mouse and humans . Sadly the links to the Kabat and Wu database in some of these papers does not point to any meaningful location. The resulting google and pubmed searches to find this lost data greatly increased the time and effort required to design my cloning experiments. Which brings me to my question. In an era when we have free wiki hosting , 4 GB free email access , supercomputers that power maps , gigabyte large free image sharing applications, $6 per month, terabyte bandwidth web hosting. Why are we still so far from an advertisement supported “free” app host for meaningful scientific data ? Perhaps its because only a few thousand people who are saving a rare turtle species somewhere on this planet will find tiagos web-app useful..Surely thats not yet worth enterprise level attention, or maybe we should all just write our web apps to run off facebook! (Source: The Omics world) The Omics world blogs http://www.medworm.com/rss/comments.php?id=927877 Thu, 04 Oct 2007 16:37:38 +0100 927877 http://harijay.wordpress.com/2007/10/03/refseq-and-uniprotkb-groups-collaborate/ 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 now I can easily linkout to the wealth of protein information provided at uniprot from my NCBI search results. This simple announcment also brings to the fore once again the complex inter-relationships between a lot of life-science data and why I dont think there will ever be a single google styled life-science database. (Source: The Omics world) The Omics world blogs http://www.medworm.com/rss/comments.php?id=925293 Wed, 03 Oct 2007 17:11:39 +0100 925293 http://harijay.wordpress.com/2007/09/19/the-rich-pdb-interface-explained/ 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://harijay.wordpress.com/2007/09/17/why-are-our-bioinformatics-workflows-so-complicated/ Why are our bioinformatics workflows so complicated! 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 maybe the primers I used to clone my CDRs from my mouse kappa light chains were probably mis-priming ( Value 10 : Ease 9) # Use pubmed to look at precedents i.e analyze all possible papers which had sequenced the mouse anitbody kappa light chain CDR region as I had attempted to do and derive the sequences of the primers they had used. It took forever to get the right keywords to query and I still have only three kappa light chain primer sequences. ANd they are all different! ( Value 10 : Ease 1 ), # Use my primer sequences , compare them with the literature and figure out how I had misprimed and why my sequences were all either of two types ( Still in progress Value immense : Ease 1 i.e still difficult to do) # Use pubmed / NCBI genome to understand the sequence space for mouse kappa light chains ( Value 10 , Ease 4 , ) # Use EBI to get the same sequence data ( Value 10 : Ease 8 ) This is still work in progress . But to summarize - The pubmed steps were the most painful . Pubmed search has to improve!. Jalview contributed the most value. For a free App its a must have in any bioinformatics toolkit!. DNAstar played its role ..but for its cost ( a few thousand dollars )! It sure gave a lot less value than Jalview All of this begs the question! ..why are bioinformatics workflows so difficult! We are a long ways away from making these things easy to do for everyone! (Source: The Omics world) The Omics world blogs http://www.medworm.com/rss/comments.php?id=877652 Mon, 17 Sep 2007 16:03:16 +0100 877652 http://harijay.wordpress.com/2007/09/14/the-restful-ncbi-query/ 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 del.icio.us with tag metagenomics you would query the URL http://www.connotea.org/tag/metagenomics Or on del.icio.us  the URL http://del.icio.us/tag/metagenomics I dont yet know how extensive the possibilities of such querying of the NCBI are,  but it looks so much easier than understanding equery. Ref: NCBI resource locator. (Source: The Omics world) The Omics world blogs http://www.medworm.com/rss/comments.php?id=872160 Fri, 14 Sep 2007 17:46:27 +0100 872160 http://harijay.wordpress.com/2007/09/13/ncbi-oddities/ 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 detailing the features of uniprot beta at this link on Bioscreencast.com . Do check it out as well as Erics comments below. (Source: The Omics world) The Omics world blogs http://www.medworm.com/rss/comments.php?id=869532 Thu, 13 Sep 2007 22:34:51 +0100 869532 http://harijay.wordpress.com/2007/09/11/video-in-science-my-foray-into-the-secondlife-metaverse/ Well I had talked about how Deepak went to SciFoo recently. It turns out that some of this years SciFoo alumni led by the indomitable Jean Claude Bradley (JCB or Horace Moody ) started the “metaverse” version of these sessions on the Nature Island on Second Life called Second Nature. In keeping with the “non conference” format of the original, session themes at SciFoo Lives On are decided on by the attendants , in this case on the wiki that serves as its permanent home outside of Second Life. Yesterdays session was on the role of “Video in Science” and of course we were there with Deepak as Whitewizard Chemistry and myself as Vishwaroop Baroque. As I awkwardly bumped into the attendees thanks to my terrible gaming skills , the whitewizard chemistry told the audience about bioscreencast.com. This was followed by a talk by JCB on “YouTube and the Sciences” and finally one from someone at the SciVee project. This was my first time in Second Life. I entered as a skeptic, since I always thought second Life is just a toy for gaming geeks and uber nerds. But I must say the poster session was just like the real thing with some added benefits. Like in the real thing, the questions made the poster session come alive but this time you get a text transcript of all conversations that took place and an overall rich experience. Not to mention the fact that the poster lives on on the NPG island and does not end up in my lab storage area ( read trash can). I came away convinced that activities like this have a great value in enriching the online scientific experience. Bertalan, one of the attendees, live blogged the event. You can catch also read about the goings on at Deepaks bbgm blog  and of course on the bioscreencast.com blog. (Source: The Omics world) The Omics world blogs http://www.medworm.com/rss/comments.php?id=861825 Tue, 11 Sep 2007 07:20:56 +0100 861825 http://harijay.wordpress.com/2007/09/08/sequence-first-ask-questions-later/ 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 microarray experiment is seeing the images on the web .. I was just wondering aloud..I am hardly an expert Addendum: There is of course no denying the added benefits of the metagenomic approach . Like the many other conclusions the paper made possible- that mite levels in both CCD and non-CCD samples were similar , that microflora ( like the bacteria in the bee gut) among Australian and American bees are similar . So I guess the question then is ..maybe metagenomics is just so much more direct that its going to be the first choice in all such open ended questions like ” What causes infectious Disease X” (Source: The Omics world) The Omics world blogs http://www.medworm.com/rss/comments.php?id=852533 Sat, 08 Sep 2007 17:54:26 +0100 852533 http://harijay.wordpress.com/2007/09/07/metagenomics-gives-clues-to-a-three-year-problem-affecting-bees/ 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 bees and considering the social structure of bees the colony withers away. Without bees there is no pollination and without pollination agriculture will suffer..and without agriculture ..well there will be no food. Scientists have therefore been struggling to find out why these colonies were collapsing and the bees disappearing ever since the first signs of CCD appeared in 2004. In the paper by Cox-Foster et al in Science Magazine ( Science Express) scientists obtained by pyrosequencing DNA sequence data from CCD and non-CCD bees from the US and Australia as well as DNA from royal jelly from china . The strategy they followed was to first get all the sequence data from CCD and non-CCD bee pools and then look for unusual sequences for bacteria and viruses and other pathogens which may signal an infection. Once the sequence data was obtained they got some initial clues as to the component foreign sequences in these pools. The final pathogen quantitation was obtained by directing PCR primers designed using the asembled metagneomics derived sequence against RNA pools from both samples. Of all candiate pathogens an as yet unclasified virus from the dicistroviridae family called the Israeli Acute Paralysis virus ( IAPV) was the only one found predomiantly in the CCD samples. The IAPV is a relative of the KBV ( Kashmir Bee virus) and ABPV ( Acute Bee Paralysis virus) and possibly represents an emergent virus that is causative agent of the colony collapse disorder. This combination approach - i.e metagnomics to get at raw sequence data followed by precise diagnostic primers and QPCR is a powerful approach which I am sure will significantly cut down the time to identify the causative agents behind future emerging infections in all organisms including humans. The rate limiting step would be the time it takes to get the metageomic sequence data which promises to get shorter and shorter. References: the bbgm article and the article in BioIT world . The paper in Science by Cox-Foster DL et. al. Other feathers in the metagenomics cap in the sequencing of large segments of the Neanderthal genome (Source: The Omics world) The Omics world blogs http://www.medworm.com/rss/comments.php?id=849992 Fri, 07 Sep 2007 16:23:22 +0100 849992 http://harijay.wordpress.com/2007/07/17/lets-open-up-science-now-letter-from-26-nobel-laureates-to-the-us-congress/ The letter  dated July 13 2007 , signed by 26 nobel laurates starts thus. “As scientists and Nobel laureates, we are writing to express our strong support for the House and Senate Appropriations Committees’ recent directives to the NIH to enact a mandatory policy that allows public access to published reports of work supported by the agency. We believe that the time is now for Congress to enact this enlightened policy to ensure that the results of research conducted by NIH can be more readily accessed, shared and built upon ­ to maximize the return on our collective investment in science and to further the public good” Read the entire letter here. But here are the key points The signatories object to barriers that “hinder , delay or block the spead of knowledge supported by federal tax dollars” A large amount of research continues to be inaccessible The Voluntary policy ( requiring a submission to PubMed Central) has not worked. Its time to make it mandatory! Several counties already do this and despite making this mandatory science has not suffered. And finally “Journals will continue to be the hallmark of achievement in scientific research, and we will depend on them.” Saw this first on Savas Parasatidis’s blog . Powered by ScribeFire. (Source: The Omics world) The Omics world blogs http://www.medworm.com/rss/comments.php?id=740473 Tue, 17 Jul 2007 15:30:17 +0100 740473 http://harijay.wordpress.com/2007/07/13/back-on-the-ncbi-horse/ 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 alignment. I could find almost 640 of them at the NCBI using the NCBI web service. All it took was understanding the existence of the deprecated uniprot id. When I similarly tested the EBI web service for the same 742 sequences, only 582 sequences were obtainable in the uniprotxml format from the uniprotkb database. As a final try , looking for some of the sequences that were missing in the better performing NCBI database , by doing a google search returned a match in the first few results. So google still is quite amazing in its ability to index even probably poorly page-ranked words like Q40LF7_DESAC. Surely the day they take on bioinformatics in a formal way will be a fun day to look forward to. references : bbgm on a Google for Bioinformatics Powered by ScribeFire. (Source: The Omics world) The Omics world blogs http://www.medworm.com/rss/comments.php?id=733676 Fri, 13 Jul 2007 20:51:13 +0100 733676 http://harijay.wordpress.com/2007/07/02/exciting-times-on-the-science-web-timo-hannay-on-nascent/ 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 podcast I am now even more inclined to pick up my print copy, to follow up on something exciting I heard on the nature podcast. Apart from the ability of audio and video to organize and nucleate communities, Timo also talks about Databases as being the conduits that enable collaborations and the role that publishers have in building communities . Towards this Natures several Gateways , are database driven community resources that aggregate content from both the community and NPG journals in several areas. The article makes good reading and I will not paraphrase it any further If I were to rank the web offerings from Nature in terms of their value to my current scientific life..my ranking would go thus 1) The Nature podcast 2) Connotea 3) The Nature Omics gateway Powered by ScribeFire. (Source: The Omics world) The Omics world blogs http://www.medworm.com/rss/comments.php?id=710290 Mon, 02 Jul 2007 18:25:22 +0100 710290 http://harijay.wordpress.com/2007/06/28/bioscreencastcom-screencasting-for-the-life-sciences/ 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 powerful medium of screencasting. This is just a beta and needless to say we need you to give us all the feedback you can.  So Dive in , check out our blog and let us know what you think. References: Bioscreencast.com Blog Another post from one of us (Deepak Singh) And last but not the least The Bioscreencast.com website . (Source: The Omics world) The Omics world blogs http://www.medworm.com/rss/comments.php?id=703096 Thu, 28 Jun 2007 20:36:33 +0100 703096 http://harijay.wordpress.com/2007/06/25/nature-precedings-a-great-offerring-from-the-npg-stable/ 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 science findings related to published work anywhere, which can then be commented on and discussed. More interestingly the FAQ page, informs us that the Nature publishing group Journals do  accept material that is in the un-peer-reviewed form and that has appeared in the preprint form : So if i get together a manuscript , I can first post it on Nature precedings and then send it for consideration to Nature for review separately and nature would still consider it ( if it meets its other criteria of course). So  this site could be a great place to establish the provenance of ideas, i.e I have a great new finding , I am gutsy enough to write it up in some form , post it on Nature precedings ..and then a few months later send the finished work to a print journal like a Nature publishing group journal that would accept it. With all of this Nature precedings has the great potential to become an online repository of pre-print findings , supplementary material and other content of use to the science community…I really cant wait for the first paper to make it from Nature Precedings to the real thing , Nature itself with a citation that first appeared online!. Powered by ScribeFire. (Source: The Omics world) The Omics world blogs http://www.medworm.com/rss/comments.php?id=694201 Mon, 25 Jun 2007 13:19:26 +0100 694201 http://harijay.wordpress.com/2007/06/20/why-google-may-be-better-to-find-uniprot-sequences-than-the-ncbi/ 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 realized that the EBI indeed does indeed serve up all of entries. SO there are a subset of uniprot entries that the NCBI does not have in its database. Out of sheer curiosity I entered the queries that drew a blank at the NCBI into Google. Wonder of Wonders google pulled up all of the hard to find UniProt entries as the very first Match.Thanks to the increasing use of publicly accessible web service APIs , Google is becoming more and more aware of a lot of very specific sequence data. I will be very happy when I can type Q57T52_SALCH calc=MW and get an answer back from right inside google. Maybe that day bioinformatics will move one step closer to becoming just another tool. Till then I am stuck with learning about Equery and WSDL and SOAP and so on.. Powered by ScribeFire. (Source: The Omics world) The Omics world blogs http://www.medworm.com/rss/comments.php?id=682876 Wed, 20 Jun 2007 18:59:42 +0100 682876 http://harijay.wordpress.com/2007/06/05/error-bars-and-experimental-biology-and-the-bbgm-podcast/ 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 fifth edition of his podcast. It was a lot of fun and I did get to talk a little about screencasting which is what we have been spending a fair amount of time on. He also got me hooked onto the TED talks, I would recommend these very enthusiastically. I was fascinated by a TED talk about photosynth and seadragon by Blaise Aguera Y arcas from Microsoft. I am very excited at the “how” , of this technology since it shares many similarities with single particle image processing and electron cryomicroscopy. Check out the bbgm podcast here. (Source: The Omics world) The Omics world blogs http://www.medworm.com/rss/comments.php?id=658928 Tue, 05 Jun 2007 15:31:37 +0100 658928 http://www.nature.com/nature/podcast/v443/n7110/nature-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 reproducing bug or virus. The ability to synthesize large amounts of large DNA :In his talk Craig Venter talked of their work in synthesizing the genome of Phi-X174 fully in two weeks. The final piece of the puzzle comes from being able to assemble stretches of synthesized DNA quickly and combinatorially from these pieces. Here the amazing bug deinococcus radiodurans comes to the rescue. Deinococcus radiodurans is able to re-assemble its genome thousands of small bits which result from very harsh radiation or severe drying. Exploiting its mechanism to achieve this amazing feat its should be entirely possible to fully reconstitute an intact genome from a multitude of pieces. The final piece of the puzzle of course is the genomics toolset itself. It is possible to assemble specialized subsets for any desired function by comparing genomes that carry out a particular function with closely related ones that do not. So given all this,  Craig Venter talks of assembling million chromosomes per day and transplanting these into cells or synthetic cells and screen for a desired effect. This he dubs as the emerging field of combinatorial genomics. A few of these desired functions are the stuff of biotechs promise since its inception: making hydrogen from photosynthetic bacteria, digesting cellulose to make ethanol and making small molecules by metabolic pathway engineering. There is more on the technological aspects of combinatorial genomics at syntheticgenomics.com , one of Craig Venters companies. The TED talk above is also an excellent listen. Other resources: The Nature podcast section on deinococcus radiodurans and mp3 file (Source: The Omics world) The Omics world blogs http://www.medworm.com/rss/comments.php?id=654483 Sun, 03 Jun 2007 07:48:30 +0100 654483 http://www.nature.com/nature/journal/v446/n7136/extref/nature05744-s2.mov I recently went to a talk given by Karl Deisseroth of Stanford University whose lab has been in the forefront of developing tools that allow neurons to be activated or de-activated using pulses of light in combination with expressed opsin transgenes. The opsins are basically photoactivated proteins ( like the rhodopsin in our retina) and they are activated by a single photon of light . Deisseroths lab had a while ago developed the use of a Channel rhodopsin- ChR2 which showed a light activated cationic (positive ion) current . Thus, when ChR2 was expressed in neurons a flash of blue light triggered a current of sodium and potassium ions which resembled the neuron firing or the action potential. The group set out looking for opsins that had the opposite effect , i.e they accelerated the suppression of the neuronal action potential ( or brought the neuron back to rest) in response to a light photon. The protein had be functional in neurons and also bring about the light activated depolarization at a time scale of the action potential . After trolling through a few opsins the Deisseroth group in close collaboration with the Georg Nagel lab at the University of Wuerzburg in Germany zeroed in on the opsin from Naturomonas pharaonis (NpHR or Halo) an archaebacteria that lives in transient salt lakes in the Egyptian dessert in salt concentrations as high as 3.5 M NaCl and a pH of 11. The bug possibly uses the opsins to capture the energy from sunlight and uses the energy to drive the uptake of chloride which allows it to survive in the very salty lake it lives in. This new opsin now was able to drive a chloride current on photoactivation which effectively turned the neuron off. Fortunately for the group the NpHr opsin was also activated at a wavelength entirely different from the “on switch” ChR2 opsin. Concurrently with the publication in Nature the group released a video of a worm expressing both opsins which could be paralysed and tickled into movement by pulses of light that stimulated NpHr and CpHr respectively. In the talk Deisseroth also spoke of developments to move the experiments into a mouse model where a transgenic mouse would have a fibre optic probe inserted into its head that would then allow light to stimulate a precice area of the brain ( like a pulse of light would cause the neuron that controlled whisker movement to turn on and the mouse would twitch its whisker). All of this clearly opens the road to other such opsins that can possibly respond to other wavelengths and drive excitatory and stimulatory currents with different properties. Interestingly way back in 2004 the metagenomics initiative by Craig Venter (the Sorcerer II expedition) published details of several novel opsins from the sargaso sea mass sequencing samples. Who knows , maybe the next such opsin may come some deep sea archaeon and have totally different spectral and kinetic properties which would allow an added level of control to the optical querying of neuronal circuits. Video of light stimulated supression of worm twitching upon NpHr (Halo) activation NpHr genome project page PlosBiology paper by Xue Han and Edward Boyden Image link from an article in the MIT technology review MIT technology review article on ChR2 and NpHr ( worm video link ) Request the ChR2 and NpHR (Halo) plasmids deposited by the  Boyden lab at addgene  (Source: The Omics world) The Omics world blogs http://www.medworm.com/rss/comments.php?id=645067 Tue, 29 May 2007 19:05:55 +0100 645067 http://harijay.wordpress.com/2007/05/17/university-knowledge-beyond-authority/ I have recently started attending the Berkman Centre Thursday Blog group meetings. The meetings which are open to the general public were started many years ago by Dave Winer and colleagues and are loosely structured to discuss topics related to blogging, the social web and also recently ( since I have been attending) entrepreneurial activity in the web 2.0 space from local startups . At the meeting I heard from Mike Walsh of a conference to be organized by the center titled , University- knowledge beyond authority. The conference aims to “generate questions, insight and solutions from diverse perspectives across the landscape of University, with a focus on the role of University as an institution.We seek to establish University as a collective force much like ‘Government’ or ‘Private Enterprise’ in its ability to negotiate and compromise for our needs in the digital environment.” The conference has several sessions dealing with topics ranging from fair use , open-access to discussing the relationships between “University” and library and the RIAA. The concept of University it seems is to organize thought and opinion on these topics from an educational perspective. Since I know very little about the complex world of licensing , and the DMCA is almost a four letter word to me, it will be fun to listen to how this concept of University evolves at University. Powered by ScribeFire. (Source: The Omics world) The Omics world blogs http://www.medworm.com/rss/comments.php?id=612185 Thu, 17 May 2007 16:18:12 +0100 612185 http://harijay.wordpress.com/2007/05/16/raindance-and-genomics-20/ 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 for moores law like advancements in such platforms bringing the genomics world closer and closer to the IT world and are all part of a revolution, Rothberg dubs as “genomics 2.0″. Powered by ScribeFire. (Source: The Omics world) The Omics world blogs http://www.medworm.com/rss/comments.php?id=612186 Wed, 16 May 2007 14:29:13 +0100 612186 http://harijay.wordpress.com/2007/05/15/academic-plasmid-sharing-made-easy/ 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 invaluable. I don’t know how long addgene has been around, but it will be quite something if the NIH made it mandatory to have all plasmids used in published work deposited at such a service. While it is still a little involved to get plasmids from addgene, since it does involve some paperwork exchange, there is no denying the fact that a central managed repository such as addgene.org will ease the load for both end user and innovator labs as well as tech transfer offices. Powered by ScribeFire. (Source: The Omics world) The Omics world blogs http://www.medworm.com/rss/comments.php?id=612187 Tue, 15 May 2007 16:55:17 +0100 612187 http://harijay.wordpress.com/2007/05/11/the-resistome-the-superbug-arsenal-characterized/ I have heard of many large scale omics studies and their resultant “omes”, but it was only last week when I was reading a review in the Journal Cell on drug resistance in bacteria did I chance on a reference to the soil bacteria resistome , which was published by De Costa et. al. almost a year ago. The paper deals with mapping the spectrum of antibiotic resistance among 480 streptomyces , the bacteria that produce several of the classes of antibiotics to kill other soil dwelling microbes. These microbes also encode a myriad of resistance mechanisms to make sure they survive the battle themselves. The resistance mechanisms brought into play by these soil dwelling bugs mimic those seen in clinically relevant bacteria. Given that its more a question of WHEN and not IF most of these mechanisms will surface in the clinical world.Therefore characterizing the diversity and density of resistance mechanisms prevalent in the environment is of extreme importance makes their study extremely relevant given the emergence of many super-bugs worldwide. The most surprising finding of the study was the diversity and density of resistance mechanisms present across all the strains. The paper tested resistance to 20 different antibiotics belonging to every known class of antibiotics produced. Shockingly several of the bacteria were resistant to all 20 of them , with the average bacterium resistant to at least 7 different classes of antibiotics. Some of the antibiotics tested, were ineffective in almost 100% of the cases . Surprisingly the newly launched daptomycin which is effective against some multi-drug resistant microbes found in hospitals etc, was inactive in almost all of the soil isolates. The authors also tested the resistome for possible mechanisms of inactivation and offered the possibility that possible novel mechanisms as well as variations of known mechanisms were operational and present in the resistome. The resistome illustrates how clever micobes are at outsmarting even the most well thought out antibiotic. Before we even think of creating an antibiotic to rule over all antibiotics , the chances that resistance to it is lurking in some niche in the microbe world seems to be quite likely. Although the resistome cannot predict how likely these resistance mechanisms are to transfer from the soil to a bug that can create problems when it sweeps through a hospitals ward: But it does make a case for using modern tools to address possible drug discovery in this class of drugs that indeed introduced chemotherapeutics to the everyday people. Superbugs have been the stuff of many a popular cover story. Drug resistant tuberculosis , cholera , malaria etc continue to wreak havoc in the developing world. Recent articles in Nature and other journals spoke of the trials and tribulations of platensimycin , the only new class of antibiotic to be discovered in nearly two decades. Even that was hardly “resistance proof” in that over-expression of its target protein was able to confer resistance to the bug. Although the resistome, you could argue makes the case for the absence of a resistance proof antibiotic it definitely underscores the importance of improving the diversity of our arsenals against infectious bacteria. Given that our pace of discovery of antibiotics seems to be slower and slower, the resistome puts some quantitative muscle behind the cries for renewed drug discovery efforts in this area. Image courtesy  Dr Gerry Wright Lab homepage (Source: The Omics world) The Omics world blogs http://www.medworm.com/rss/comments.php?id=603049 Fri, 11 May 2007 21:28:19 +0100 603049 http://harijay.wordpress.com/2007/04/20/blogs-that-make-me-think-or-a-post-from-a-fan/ 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: Deepak first blogged about this company on his bbgm blog. Following which I also heard one of its founders interviewed by Jon Udell. Following these postings,I was hooked. Juice’s approach to analytics using Excel has made me start appreciating the power of analytics (for eg check out this post analysing the above podcast interview) 3)Jean Claude Bradley: Early on Jean Claude Bradley commented on one of my posts, following which I checked out his useful chemistry blog. His championing of the power of the wiki , his approach to chemistry education and dedication to open-science are inspirational. Jean Claude Bradley also introduced be to youtube as a means of science popularization. 4) Pierre Lidenbaum at Yokofakun: I started reading his blog after using his pubmed2connotea greasemonkey script. Pierre bioinformatics posts excite the wannabe coder in me. 5 &6 ) For the last blog, I would like to trackback to two blogs that are examples of science blogging at its best. They are the John Hawks anthropology blog and Damian Allis’s blog, also tagged by Deepak. Both of these blogs make me want to be a better “scientific” blogger and were instrumental in making me take the blog plunge. I particularly enjoyed readings John Hawks coverage of the “hobbit man” findings and the visual appeal of Damians Allis’s blog ( I confess I am no computational chemist). Before I go I will repeat here the rules of the Thinking blog tagging chain ,copied from Deepaks post: (1) If, and only if, you get tagged, write a post with links to 5 blogs that make you think; (2) Link to this post so that people can easily find the exact origin of the meme; and (3) Optional: Proudly display the ‘Thinking Blogger Award’ with a link to the post that you wrote. (Source: The Omics world) The Omics world blogs http://www.medworm.com/rss/comments.php?id=556957 Fri, 20 Apr 2007 17:37:20 +0100 556957 http://harijay.wordpress.com/2007/04/01/membrane-protein-crystallization-analytics/ 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 . But talking of analytics , I recently came across the very appropriately named “Membrane protein databank” which has a lot of compiled and elegantly displayed statistics on every aspect of membrane proteins structural biology ranging from the the expression systems and source organisms used to the detergents , additives and phasing methodology used for structure solution. The MPDB seems to be a manually curated database which relies on the efforts of its creators to keep it up-to-date and accurate. As we all get increasingly open to sharing data pre and post publication . It will be exciting to see compilations like the MPDB emerge in the empirical and trial and error world of protein expression and crystallization trials . The advantages of using web2.0 frameworks to share and store information of the kind contained in the MPDB is exciting. I cant wait for the day that a live RSS feed on my personalized google homepage informs me of the fact that Tim Toolman from the University of Xtal has crystallized a CLC channel from Halothermotrix orenii by expression in archaeoglobus fulgidus and it simultaneously updates a live graph of the many parameters used in these experiments probably available as a desktop widget on my google toolbar. (Source: The Omics world) The Omics world blogs http://www.medworm.com/rss/comments.php?id=515190 Sun, 01 Apr 2007 11:05:26 +0100 515190 http://harijay.wordpress.com/2007/03/30/blink-and-its-done/ 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 BLAST results (blink) page for that GI. This interface is very powerful and a great way to explore the sequence space for any protein. I have put together a screencast documenting one of my recent explorations you can see it on the youtube link above. Documentation: The Blink documentation (Source: The Omics world) The Omics world blogs http://www.medworm.com/rss/comments.php?id=511400 Fri, 30 Mar 2007 18:29:48 +0100 511400 http://harijay.wordpress.com/2007/02/03/why-i-think-the-ncbi-rocks/ 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 staff at NCBI who attempted to help me troubleshoot the search pattern. Often these conversations lasted almost 30-40 minutes and contributed immensely to my knowledge of how the NCBI was laid out , the numerous interconnected databases , the precompiled BLAST options , the linkout options and the MyNCBI “personalization” options. Before this encounter, I did on many an occasion found myself hoping that google would index all the biomedical information out there and make a lot of it available in a “google-ized” format. I am beginning to change my mind on this. Having realized the powerful ways of querying the data at NCBI . I can certainly say that I turn to the NCBI more and more to construct and optimize several queries in the genomic sequence space. The dedication with which the NCBI support staff pursued my problem is something I have only come across on many open-souce forums. In direct contrast a few of my posts to google “support” to get some basic questions on their Google calendar bugs sorted out were largely ignored. Vertical search is becoming a huge buzzword in this web 2.0 aroused world. Lets face it the NCBI had been our vertical seach platform. Its been around long before the term “search” meant what it is today. It is comprehensive, cross-referenced and annotated to the hilt , has personalization , RSS feeds , email alerts , links to full-text and private libraries all built in for FREE. In my very humble opinion it has evolved into an extremely powerful and dare I say user-friendly front end to query all biomedical information. If only more of us Omics practitioners take the time to learn its very powerful features. I for one will definitely try to blog more about its many facets ( along these lines see Search in the Omics age, Compiling search strategies in the biosciences, Screencast 101 ). And I will never wish google waste its time with what the NCBI has already done so well. I only wish the NCBI would popularize its offerings more. I also wish all the bioinformaticians out there would do their part in teaching everyday users the ins and outs of its tools. For now I am glad that we have something a powerful and dedicated as the NCBI. (Source: The Omics world) The Omics world blogs http://www.medworm.com/rss/comments.php?id=485790 Sat, 03 Feb 2007 18:21:08 +0100 485790 http://harijay.wordpress.com/2007/01/02/the-abc-transporter-retraction/ (more…) (Source: The Omics world) The Omics world blogs http://www.medworm.com/rss/comments.php?id=485791 Tue, 02 Jan 2007 13:01:00 +0100 485791 http://harijay.wordpress.com/2006/12/11/compiling-search-strategies-in-the-biosciences/  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. Assuming this ability is learned and not innate, the post says it will be very useful to compile effective strategies to understand what is it that makes a good search strategy. Jon Udell started a tag called searchstrategy on del.icio.us to compile his list.   I too started one on del.icio.us called ncbi-serach-strategy to hopefully compile my own list that will be more bioscience specific. Maybe by such tag aggregation , we can all start to learn at what is it that makes a good search strategy. I would definitely recommend reading Jon Udell’s post and the comments therein , and also hope this practice of compiling search strategies catches on  as we all learn to handle the gigabytes of omics information. refs : Google Hacks  Search , in this Omics age See “Search in this Omics age” (Source: The Omics world) The Omics world blogs http://www.medworm.com/rss/comments.php?id=485792 Mon, 11 Dec 2006 19:40:44 +0100 485792 http://harijay.wordpress.com/2006/12/11/search-in-this-omics-age/ 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. In addition , there was no genomic DNA for yersinia pusedotuberculosis, but I could get genomic DNA for another member of the yersinia genus Yersinia enterocolitica . Since we always prefer to PCR from genomic DNA I decided to look for whether Y. enterocolitica had the same protein. So here was my search strategy and the results obtained- Query the NCBI database to learn that the genome is still unfinished since the sequence for only a few plasmids were present - partial success Next from the genome link I got to the information on the genome and learned of the use of an NCBI field query [orgn] as in txid630[orgn] - partial successI then used the linkout from the Lineage line which took me to the Sanger institute center which was sequencing the Yersinia enerocolitica type :08 genome and tried to BLAST my sequence against that genome but could not find yersinia enterocolitica in the list there - failure 3. I then went back to the genome page and found a link to a different Genome project for the bug , this time at the Walter Reed Army Institute. This time the “BLAST genome” link led me to another NCBI page with a direct plugin into running a BLAST query against the genome - success 4. I then pasted in the protein FASTA sequence of the particular protein I was interested in and tried to run a blast and I got an error which said “INFO: No alias or index file found for component [Microbial/630], type [protein] in search path [/export/home/splitd/blastdb/blast1:/blast/db/disk.blast/blast1::]”. This seemed more like a database error than a failure to find the sequence in the bug - failure So in the end I was just confused and learnt not to go looking for homologs among unfinished genomes and considered my time wasted. I then read a post from Jon Udell titled - “Hunting the elusive search strategy” in that post Jon talks about how some people are actually willing to pay “tech support” $100 for running a Google search and further that “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.” This made me re-evaluate my earlier appraisal of my two hours as “time wasted”. For sure , I will always now look at the “linkouts” mentioned above for future searches. All of the pages I navigated through are now part of my reservoir of tacit knowledge. These are hopefully intergrated into my future search methodology. Jon Udell also proposes to compile a list of his search strategies as part of two del.icio.us tags. So to hope that this practice catches on. I will start my own collection here. Now, I only hope someone pays me $100 to run such a search in the future. powered by performancing firefox (Source: The Omics world) The Omics world blogs http://www.medworm.com/rss/comments.php?id=485793 Mon, 11 Dec 2006 18:52:14 +0100 485793 http://harijay.wordpress.com/2006/11/04/systems-biology-education-bringing-the-quantitation-to-biology/ Nature reviews Cell and Molecular Biology has an excellent freely accessible supplement called the systems biology user guide. In it are various sections that talk of the applications and challenges facing systems biology. One of them is an essay on education for systems level biologists titled “Back to the future.” The essay talks of how the graduate level scientists are hardly trained to appreciate the interdependence of modern research on concepts across physics mathematics and biology.  Thus most undergraduate science majors regardless of their ” concentration” don’t really know much of  disciplines outside of  hwat they focus on . Consequently later at the graduate level, they are quite at a loss working on problems like systems biology which clearly require a firm grasp of concepts across all of these disciplines. The article addresses the  question of the time and format to teach these concepts to future scientists and concludes that an undergraduate introductory class in biology is probably the best time to commence such an education. Wingreen and  Botstein then relate their experiences in conducting a seminar class at Princeton which was targeted at early graduate students made up of a mix of students with biology, physics and math backgrounds. The Seminar class used classic papers from early and relatively recent “Biology” that drew on skills across the three fields . Each paper represented a major breakthrough in Biological understanding due to a combination of keen mathematical and physical insights applied to a biological observation. Interestingly almost all these classical papers came from the 1940s to 1990s, a time that the authors observe ” biologists’ and physical scientists’ educations were less different than they are today”. The seminar course at Princeton  serves as an interesting model to educate future graduate students to prepare them to function and research in the systems world.  A lot of the lessons in these early papers are curiously being re-learnt by modern day practitioners of systems biology. I think it will serve anyone wishing to appreciate the systems perspective immensely  to re-read some of these classic papers. I for one being a trained reductionist plant to go and read all of these classic papers and attempt to “re-educate” myself . Hopefully this will help me get a better grasp of the systems approach and develop a more quantitative frame of mind. refs: Mol 515 at Princeton Back to the future : education for systems level biologists (Source: The Omics world) The Omics world blogs http://www.medworm.com/rss/comments.php?id=485794 Sat, 04 Nov 2006 21:08:25 +0100 485794 http://harijay.wordpress.com/2006/10/31/the-coming-deluge-google-buys-jotspot/ 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 Google Docs & Spreadsheets and Google Groups.” All of this signal Googles move into the ongoing wave of enterprise wiki service applications. refs: Moving ELNs offsite Update: Clearly the acquisition of Jotspot by google has everyone very excited . Check out the responses here  (Source: The Omics world) The Omics world blogs http://www.medworm.com/rss/comments.php?id=485795 Tue, 31 Oct 2006 18:19:51 +0100 485795 http://harijay.wordpress.com/2006/10/22/screencast-101-windows-media-encoder/ 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-pro to compress them. Both ISHOWU($20) and quicktime pro($30) are not free software unlike WME. It will be great if Apple adds some screencast support into its OS X. In any case you can see my test screencast here. This is a wmv file simply uploaded to a webserver. You can shift click the link , save it to your computer and view it using windows media player or suitable *.wmv player. This video is the best quality but needs to be saved to disk before viewing. * Following a brief from Jean-Claude Bradley I have uploaded both MAC and PC versions of the videos onto YouTube and Google video . The video quality on both is barely passable once processed by either service. The uploaded mac video started from 27 MB and the wmv started at 1.56 MB but both end up quite hazy and unclear. This is work in progress. Google Video : Mac screencast with IshowU and the Windows WME screencast : YouTube Video: Mac screencast with IshowU and Windows WME Addendum: I am convinced on the utility of using youtube to share screencasts. The screencast below is the same as that mentioned above and made in windows media encoder. The text quality is quite poor , but the ability to embed these videos with just a simple tag from youtube adds a whole new dimension to blogging (Source: The Omics world) The Omics world blogs http://www.medworm.com/rss/comments.php?id=485796 Sun, 22 Oct 2006 18:07:23 +0100 485796 http://harijay.wordpress.com/2006/10/19/a-blog-ressurected-screencasting-a-great-thing/ 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 list of screencasts  which illustrate the power of the medium. You can also check out his del.icio.us tag and the very good howto he has put together on making such screencasts using windows software . Screencasting,  I do believe will truly change the communication landscape and narrow the gap between “geek” and everyday users of computers software. Having seen the few movies explain the functionality of web sites like Backpackit and programming environments like Ruby, I wish that every question I had about how to achieve some functionality using software was answered using a screencast. I am putting together my own collection of howtos that deal with using the NCBI site ( phew ! finally a connection to the Omics in the blog title)using the screencasting medium. For now I am sold on the utility and promise of screencasting. (Source: The Omics world) The Omics world blogs http://www.medworm.com/rss/comments.php?id=485797 Thu, 19 Oct 2006 23:42:46 +0100 485797 http://harijay.wordpress.com/2006/09/28/moving-elns-offsite/ 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 I am sure they will be indexed by search engines and thus my data will be freed from the confines of my paper and binder lab notebook. The service costs $5 and also guarantees me absolute peace of mind. Having had three machine crashes the last few months I never once winced knowing that my notebook and its contents are safe at Backpackit. Another big plus is that I have access to it from every OS I use using a very nice firefox plugin . All of this brings me to an article I read about the end of venture capital . The article talks about an IT company not very different from the lab I work in. Its a small company run by a dozen odd people which used off-site services to streamline and “virtualize” its operations. Consequently they had yahoo handle their email and site hosting and Jotspot handle their backoffice for just $15 a month( talk about value for a small business). All of this left the company with time and resources to concentrate on their main product. Importantly they did it all without spending a dollar in venture capital. Now replace the company with any typical NIH funded lab and replace venture capital with university overhead or NIH funds themselves and I really think the article has a lesson for any research lab. Just like outsourcing sequencing reactions or antibody making services, I think there is tremendous value in moving lab data archival and indexing off-site leaving me to concentrate on the research. Having all my electronic data off-site does tie me down to the network but soon I have to worry a lot less about backups or viruses in my campus network. Added to all that , if I use a service like backpackit I can make all lab-bench data public when I publish a paper with the push of a button. Now there is something to be said for that and moving ELNs off-site. powered by performancing firefox * The Business|Bytes|Genes|Molecules has a post on SAAS and utility computing. I could not agree more : there is tremendous value in virtualizing for everone ranging from small biotech to an even smaller me everyday average Joe researcher and its amazing how much all of this truly moves us closer to the SUN adage the network is the computer or an even more cliched one “The Browser is the OS” * John Udell a has a nice screencast about jotspot here (Source: The Omics world) The Omics world blogs http://www.medworm.com/rss/comments.php?id=485798 Thu, 28 Sep 2006 14:42:40 +0100 485798 http://harijay.wordpress.com/2006/09/27/great-software/ 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 are the recent technologies that have made my life so incredibly easy that they probably did represent significant achievements in software design or were probably the cumlination of people who wrote software that “did the right thing”. Using as a criteria , software or systems that I use so extensively and thoroughly that they are as much a part of me as my arms and legs , I made myself a quick “inapiration list ” in no particular order. They are Google , firefox , Microsoft Excel , a MySQl relational database , my home box running gentoo linux , the scripting language PERL and although still very new my OSX running macbook pro. I would also add the eclipse IDE to this list but that hope to be the subject of another post. And as I was checking my gmail , in came an article on the SUN developer connection mentioning the 12 greatest pieces of software ever written. The list I was very happy to note included, every item in the above list I compiled in some way shape or form. Google ( pagerank , no 11) , firefox ( well NCSA mosaic made no 6) , Excel ( no 9) , MySQL ( relational database no 2 ) , PERL ( the genome assembler coded in perl no 3) , and OSX ( based on BSD unix no 1 ) , gentoo linux ( also no 1). I guess I am smiling because atleast I know a good thing when I see it. Charles Babcock I couldnt agree more. powered by performancing firefox (Source: The Omics world) The Omics world blogs http://www.medworm.com/rss/comments.php?id=485799 Wed, 27 Sep 2006 20:17:38 +0100 485799