| News & Commentary |
BioPuppy is an open source minimal Linux OS for bioinformatics, based on Puppy Linux. It has tremendous support from all over the world. More than 500 universities/colleges and thousands of individuals have downloaded and are using it. And we have just released the second version, which includes updates and more bioinformatics applications.
AVAILABILITY:
http://www.biopuppy.org/
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This is a call for papers for an innovative medical journal to be launched in January 2010 with the birth of "The Sri Lanka Journal of Bio-Medical Informatics." The journal will be a joint official publication of The Post-Graduate Institute of Medicine of The University of Colombo, Sri Lanka and The Health Informatics Society of Sri Lanka.
This quarterly publication, presented as an exclusive e-journal, will be electronically distributed widely in Sri Lanka and abroad and bears the ISSN number 2012-6077. The journal will provide free, full text access to all registered users, completely free of charge.
FOR MORE INFORMATION:
The scope of the journal, the publication policies and many other details are available in its home page accessed by registration through the web site http://www.sljol.info/.
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It is with great sadness that we report the loss of our colleague in the field, Warren DeLano, who was well-known for the creation of the open-source PyMOL molecular graphics system. Warren was just 37 years old.
His family has set up a website where people can share memories of Warren: [link]. There is information there as well on a memorial fund that has been created in his honor for the support of future open-source software development in science.
All of us at Bioinformatics.Org offer our deepest condolences to his family at this time.
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Mining the NCBI Influenza Sequence Database: adaptive grouping of BLAST results using precalculated neighbor indexing - a knol by Leonid Zaslavsky and Tatiana Tatusova
The Influenza Virus Resource and other Virus Variation Resources at NCBI provide enhanced visualization web tools for exploratory analysis for influenza sequence data. Despite the improvements in data analysis, the initial data retrieval remains unsophisticated, frequently producing huge and imbalanced datasets due to the large number of identical and nearly-identical sequences in the database.
We propose a data mining algorithm to organize reported sequences into groups based on their relatedness to the query sequence and to each other. The algorithm uses BLAST to find database sequences related to the query. Neighbor lists precalculated from pairwise BLAST alignments between database sequences are used to organize results in groups of nearly-identical and strongly related sequences. We propose to use a non-symmetric dissimilarity measure well crafted for dealing with sequences of different length (fragments).
A balanced and representative data set produced by this tool can be used for further analysis, i.e. multiple sequence alignment and phylogenetic trees. The algorithm is implemented for protein coding sequences and is being integrated with the NCBI Influenza Virus Resource.
FULL ARTICLE:
[link]
Published in PLoS Currents: Influenza (http://www.plos.org)
REFERENCE:
Zaslavsky, Leonid; Tatusova, Tatiana. Mining the NCBI Influenza Sequence Database: adaptive grouping of BLAST results using precalculated neighbor indexing [Internet]. Version 136. PLoS Currents: Influenza. 2009 Oct 30:RRN1124.
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DATES: November 25-26, 2009
LOCALE: University of Manchester, UK
URL: [link]
Ondex is a open source data integration platform that enables data from diverse biological data sets to be linked, integrated and visualised through graph analysis techniques. It has the ability to bring together information from structured databases and unstructured sources, such as free text, whilst also offering a friendly user-interface to visualise and analyse integrated data.
A prerequisite to data integration and analysis is the collection and pre-processing of relevant data sources. Taverna (a component of the myGrid Project) is a workflow management system that allows users to develop and run workflows by combining distributed and local analysis tools and data resources.
The course, aimed at bioinformaticians and systems biologists, will be delivered in a blended-learning manner; both with lectures and “hands-on” workshops. We will show you how to perform common tasks using Ondex,; which methods are best suited to perform them, and how to analyse the results. In addition, we will show you how to build simple data collection and analysis workflows in Taverna; and demonstrate how the two technologies complement each other to perform a complete in silico experiment. Alongside this, we will share with you a portfolio of successful projects that have used Ondex and Taverna.
REGISTRATION:
For further information and registration please go to: [link]
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We are pleased to announce the Firefox plugin for the TexFlame service that was announced here last month. The extension detects a PubMed abstract page (by scanning the page URL) and then calls the TexFlame service, which in turn renders the abstract as a SBGN-like graph.
AVAILABILITY:
[link]
The TexFlame server itself is a separate on-line service, free to individuals.
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EMBnet.news, the official and fully open access journal of the EMBnet network, is out. The journal is now using a new publishing system that presents the journal in various formats. EMBnet.news also announces that in the coming issues it will contain a peer review section.
Highlighted articles are:
- Bioclipse 2: towards integrated biocheminformatics
- Ensembl: A New View of Genome Browsing
- Linux distributions for bioinformatics: an update
URL: [link]
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For one week, I took a stop watch and measured how much time I spent scanning the literature with I, Librarian. Here are a few numbers, so you can quantitatively compare how time-efficient the mining method that you currently use is: [link]
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DATE: October 19, 2009, 7:30-9:00pm EDT
LOCALE: Online at Johns Hopkins University
Join us at our virtual information session introducing our fully online MS in Bioinformatics degree. Find out how you can earn a Masters of Science in Bioinformatics entirely online. Learn about the program's admission requirements, curriculum design, course structure, degree requirements, and how online education works. Participate in an online discussion or chat about the program with faculty, and the associate program chair. Visit a unit from our core course "Computers in Molecular Biology" to see how course content is presented.
REGISTRATION:
Please RSVP online by October 17, 2009: [link]. You will be provided information to participate in the online information session after you RSVP and before the event.
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DATE: November 4, 2009, 10:00am-5:30pm
LOCALE: Department of Genetics, University of Cambridge, UK
URL: [link]
We will be running an introductory tutorial on designing and building Taverna workflows next month in Cambridge. The course is free to attend and is offered on a first-come first serve basis. It is a practical one-day course focusing on workflows in the Life Sciences.
REGISTRATION:
For more information, and to sign-up, please see the course website here: [link]
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| Acknowledgments |
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We wish to thank the following for their support:
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