Bio Saga Blog - A Chronicle of Life Sciences & Informatics

At the Bio-IT World Conference last week, Intel unveiled a new website, dubbed Optimized Code, that offers access to versions of several popular open-source bioinformatics analysis tools that the company has optimized to run on Intel Xeon processors, with the aim of generating results faster and more efficiently than standard iterations of these solutions. The first set of applications that the company has released specifically for genomic analysis include optimized versions of  the Broad Institute's Genome Analysis Toolkit ; Blast algorithms for nucleotide- and protein-based sequence searching; BWA-ALN , software for mapping low-divergent sequences to a reference genome; and MPI-HMMER , protein sequence analysis software. The company has also released optimized code for AMBER and NAMD, both of which are used for simulating the molecular dynamics of biomolecular systems. The Intel website provides performance numbers for each of the optimized codes as well as directions for h...

The National Center for Biotechnology Information  is asking for the bioinformatics community's input on a  proposed Blast XML specification update planned for release in the summer of 2014. The update, according to the development team, is intended to improve the consistency of the Blast output with XML standards as well as put in place new and useful elements. Blast XML users can submit their feedback at  this link .

Courtesy: Dr Raghava &  Bioclues PubDNA Finder is an online repository to link PubMed Central manuscripts to the sequences of nucleic acids appearing in them. It extends the search capabilities provided by PubMed Central by enabling researchers to perform advanced searches involving sequences of nucleic acids. This includes, among other features, (1) searching for papers mentioning one or more specific sequences of nucleic acids and (2) retrieving the genetic sequences appearing in different articles. These additional query capabilities are provided by a searchable index that was created by using the full text of the 176672 papers available at PubMed Central at the time of writing and the sequences of nucleic acids appearing in them. To automatically  extract the genetic sequences occurring in each paper an original method has been developed. The database is updated monthly by automatically connecting to the PubMed Central FTP site to retrieve and index...

The Ontario Genomics Institute has started a new fund that will be used to make genomics research papers available as open access from the date of their publications in journals. The OGI Genomics Publication Fund (GPF) will contribute up to C$3,000 ($2,900) per publication to genomics researchers in Ontario who want to make their papers available. The GPF will be open to researchers at Ontario-based academic, industry, or government institutions, and its goal is to maximize access to important genomics publications and to increase the visibility and citations of genomics research conducted in the province. OGI expects to support up to 35 open access publications over the next 12 months, and it will either reimburse special fees charged by traditional publishers to make individual manuscripts open access or to defray publication costs for manuscripts published in open access. "OGI's program is targeting those publications with the greatest potential reach. Open sharing of knowl...

BioTorrents, a website that allows open access sharing of scientific data and uses the popular BitTorrent peer-to-peer file sharing technology. BioTorrents allows files to be transferred rapidly due to the sharing of bandwidth across multiple institutions and provides more reliable file transfers due to the built-in error checking of the file sharing technology. BioTorrents contains multiple features, including keyword searching, category browsing, RSS feeds, torrent comments, and a discussion forum. AVAILABILITY: BioTorrents is available at http://www.biotorre nts.net/ REFERENCE: A complete description of BioTorrents is described in the manuscript at http://www.plosone. org/article/ info:doi/ 10.1371/journal. pone.0010071

BioSLAX is a new live CD/DVD suite of bioinformatics tools that has been released by the resource team of the BioInformatics Center (BIC), National University of Singapore (NUS). Bootable from any PC, this CD/DVD runs the compressed SLACKWARE flavour of the LINUX operating system also known as SLAX . SLAX is becoming the live CD/DVD of choice because of its ability to modularize almost any application and plug it into the system on the fly. The system can also be installed to USB thumb drives or directly to the PC as a regular Linux using the BioSLAX installer provided. It consists of commonly used Bioinformatics Applications, Software and Algorithms. For Download, http://www.bioslax.com/downloads.shtml

If you offer something of value to people for free while someone else charges a hefty sum of money for the same type of product, one would logically assume that most people would choose the free option. According to new research in the February 20 edition of the journal Science , if the product in question is access to scholarly papers and research, that logic might just be wrong. These findings provide new insight into the nature of scholarly discourse and the future of the open source publication movement. To test this theory, James A. Evans, an assistant professor of sociology at the University of Chicago, and Jacob Reimer, a student of neurobiology also at the University of Chicago, analyzed millions of articles available online, including those from open source publications and those that required payment to access. The results were surprising. On average, when a given publication was made available online after being in print for a year, being published in an open source format ...

OSDD is a CSIR-led Team India consortium with a global partnership. It's vision is to provide affordable healthcare to the developing world by providing a global platform where the best minds can collaborate & collectively endeavor to solve the complex problems associated with discovering novel therapies for neglected tropical diseases like malaria, tuberculosis, leishmaniasis, etc. It is a concept to collaboratively aggregate the biological and genetic information available to scientists in order to use it to hasten the discovery of drugs. This will provide a unique opportunity for scientists, doctors, technocrats, students and others with diverse expertise to work for a common cause.The OSDD Initiative Website www.osdd.net was launched on 15th September 2008 by...

In a paper called "Metagenome Annotation Using a Distributed Grid of Undergraduate Students" I just love this title! It's nerdy and cute, all at the same time. Says Sandra Porter . The paper describes a class where students from Marseilles University investigate the function of unidentified genes from a Global Ocean Sampling experiment. All the sequences are obtained from the environmental sequence division at the NCBI . French researchers describe their strategy for teaching undergraduate-level bioinformatics using cutting-edge genomic data and a Web-based learning tool. The students then annotated real metagenomic sequences from the Global Ocean Sampling experiment. "In return for their much-needed help sorting out oodles of DNA data, the undergrads gain a practical knowledge of the work involved in doing bioinformatics and metagenomics, and, most importantly of all, they get to experience what it's like to do real research," says Karen James at the Be...

A Subject Tracer™ Information Blog developed and created by Internet expert, author, keynote speaker and consultant Marcus P. Zillman, M.S., A.M.H.A. for monitoring biological informatics (health informatics, neuroinformatics, biodiversity informatics and biomolecular informatics resources and sites on the Internet. This blog page has a good, comprehensive listing of very handy useful bio web resource sites, the blog is divided into the following categories: BIOLOGICAL INFORMATICS HEALTH INFORMATICS (Medical Informatics) NEUROINFORMATICS (NI) BIODIVERSITY INFORMATICS (BDI) BIOMOLECULAR INFORMATICS (BioInformatics) Online Tools and Web Applications Current Subject Tracer™ Information Blogs Be a part of the XTractor community. XTractor is the first of its kind - Literature alert service , that provides manually curated and annotated sentences for the Keywords of user preference. XTractor maps the extracted entities (genes, processes, drugs, diseases etc) to multiple ontologies and en...

Recently took a peek at the new version of UniProt. It has some exciting features on customized searches, filtering results using key words, customize the results view and cross references to Public databases including the 3D- viewers. Try taking the SITE tour on the right hand side panel. http://beta.uniprot.org. This is a beta version of the their new web site, most welcome to give your feedback . Please take into account that some functions are incomplete and many help pages are still preliminary. beta.uniprot.org

The European Commission has awarded €4.5 million ($7 million) to a consortium of 32 research organizations, universities, and companies from 13 countries to determine how to transform Europe’s biomedical data resources into a transnational “sustainable integrative bioinformatics network” for the life sciences. The consortium is led by the European Bioinformatics Institute. The first year and a half of this project, called ELIXIR, for European Life-science Infrastructure for Biological Information, is aimed at gathering input, performing technical-feasibility studies, and doing user surveys among researchers who generate and use data, and develop tools. Much like the Oxford English Dictionary, which will remain useful as long as people speak English, so, too, will “the infrastructure for biological information … continue as long as people are interested in biology, health, and medicine,” she said. But provisions must be made to allow that to happen, including upgrading the infrast...

goosh.org - the unofficial google shell ( http://goosh.org /). It is pretty neat and useful in its neonatal state itself, like to read a feed, you can type, for eg: r http://www.google.com/reader/public/atom/user/11136726768885096694/label/cbn-roll and gets default 4 latest feeds, or you can check out a ncbi accession by typing, for eg: NP_001108376 and get to the Fugu fish refseq link. The most useful thing is the fact that it it text based and quite easy to parse visually as well as via scripts. Another cool feature for me right now is the shell translation, like to get the english word for the norwegian word 'hvor', all I have to do is type: t no en hvor which correctly says: translating "hvor" from "no" to "en": "where" More discussion going on at http://tech.slashdot.org/article.pl?sid=08/06/02/222234&from=rss . Enjoy!

The CDD [ http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml ] and the its search tool [ http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi ] has been recently updated. Also check out the latest approach for "automatically assigning subcellular locations" to protein from Newberg and Murphy [ http://pubs.acs.org/cgi-bin/abstract.cgi/jprobs/asap/abs/pr7007626.html ].

Ambitious plans to catalogue and characterize all proteins in the human body — a Human Proteome Project — are being drawn up by a small group of researchers. But with a price tag of around US$1 billion, some question whether the organizers can raise enough money or momentum for such an undertaking. Project aims to characterize all human proteins. Talking about characterizing human proteins; there are several organizations working around the globe towards this initiative, spanning across both the public and commercial domains. Having missed out on HGMP, this time the industry in India is all geared up towards the mapping of human proteome. Molecular Connections collaborates with Plasma Proteome Institute and with Max Planck Institute of Psychiatry, Proteomics & Biomarkers Research Group that would significantly aid them in the development of their new knowledgebase CliPro .

OpenHelix is providing free UCSC Genome Browser training for Institutions. You can apply for this at http://www.openhelix.com/seminars . "The three and half hour introductory tutorial will cover the topics needed to effectively use this powerful, free, publicly-accessible tool, including: basic functionality of Genome Browser searching and BLAT use, Table Browser use, creating and using Custom Tracks, and an introduction to the Gene Sorter. Participants will receive slide hand-outs, exercises, and a UCSC Genome Browser and Table Browser Quick Reference Cards."