| News & Commentary |
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DATES: January 28-29, 2010
LOCALE: Karunya University, Coimbatore, India
The ICMR sponsored National Conference on "Proteomic Applications: Perspectives in Healthcare" (NCPPH-09) will provide you with an excellent opportunity to present your latest research in proteomics and computational intelligence based techniques applied to problems in bioinformatics and computational biology. It will provide invaluable opportunities for academia, scientists and industry professionals to interact with each other and share experiences. NCPPH-09 is being organised by Karunya University Department of Bioinformatics, Coimbatore, India.
FOR MORE INFORMATION:
Contact: Dr. J. Jannet Vennila
Associate Professor & Head (organising secretary)
Department of Bioinformatics
School of Biotechnology & Health Science
Karunya University
Coimbatore – 641114
Phone: 0422 2614472
Email: ncpphbin@gmail.com, jannet_r@karunya.edu
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At the University of Manchester, UK, we have over 10 years experience in running a range of online courses in computational biology. These courses are designed to enable biologists and computer scientists to update their skills, while remaining in the workplace. They are also very suitable for home study, helping you to keep in touch with a research environment while taking a career break.
Following a review of our programmes we are now delighted to be able to announce the introduction of new course themes in:
- Computational Bioinformatics
- Computational Systems Biology
For further information, please visit our programme website: [link]. If you have any questions, or would like advice on the options, please contact Heather.Vincent@manchester.ac.uk.
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The ISCB Student Council is pleased to announce an internship at the Schneider Group at EMBL-Heidelberg. This internship is exclusively arranged by the Student Council in collaboration with Dr Schneider for a student from a developing nation. The goal is to train an undergraduate student in Data Integration and Knowledge Management in Computational Biology.
FUNDING:
Internship will be funded at Euros 400/month for 6 months. Student will be provided with free accommodation during his/her stay at Heidelberg. The cost of the travel to and from the home country to Heidelberg will NOT be covered by the host lab and shall be borne by the student in full.
IMPORTANT DATES:
Last date for Application Submission: Dec 20, 2009
Acceptance Notification: Jan 15, 2010
FOR MORE INFORMATION:
[link]
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ABSTRACT:
DNA microarrays are used to measure gene expression levels of genes. After microarray images are scanned and raw expression data are generated, the typical workflow of analysis is structured on six main phases: (i) summarization, (ii) quality control, (iii) normalization, (iv) filtering, (v) statistical analysis, and (vi) biological interpretation. Eg., summarization aims to recognize different genes in raw data, associating to different probes (regions of pixels in images) the unique gene that generated them. Nevertheless, many existing tools, such as the well known TMeV, part of TM4 Suite, currently are not able to automatically summarize recent arrays, such as the Affymetrix ones. micro-CS is a tool that automatizes the summarization, normalization and annotation of Affymetrix microarray data, extending the TMeV tool.
AVAILABILITY:
http://www.bioinformatics.org/m-cs/wiki/
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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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| Acknowledgments |
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We wish to thank the following for their support:
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