Computational Biology
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Computational biology and bioinformatics : Latest content : nature.com

Computational biology and bioinformatics : Latest content : nature.com | Computational Biology | Scoop.it
Computational biology and bioinformatics is an interdisciplinary field that develops and applies computational methods to analyse large collections of biological data, such as genetic sequences, cell populations or protein samples, to make new...
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Rescooped by Kasia Chyżyńska from Viruses, Immunology & Bioinformatics from Virology.uvic.ca
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Closing the loop: from paper to protein annotation using supervised Gene Ontology classification

Closing the loop: from paper to protein annotation using supervised Gene Ontology classification | Computational Biology | Scoop.it

Gene function curation of the literature with Gene Ontology (GO) concepts is one particularly time-consuming task in genomics, and the help from bioinformatics is highly requested to keep up with the flow of publications. In 2004, the first BioCreative challenge already designed a task of automatic GO concepts assignment from a full text. At this time, results were judged far from reaching the performances required by real curation workflows. In particular, supervised approaches produced the most disappointing results because of lack of training data. Ten years later, the available curation data have massively grown. In 2013, the BioCreative IV GO task revisited the automatic GO assignment task. For this issue, we investigated the power of our supervised classifier, GOCat. GOCat computes similarities between an input text and already curated instances contained in a knowledge base to infer GO concepts. The subtask A consisted in selecting GO evidence sentences for a relevant gene in a full text. For this, we designed a state-of-the-art supervised statistical approach, using a naïve Bayes classifier and the official training set, and obtained fair results. The subtask B consisted in predicting GO concepts from the previous output. For this, we applied GOCat and reached leading results, up to 65% for hierarchical recall in the top 20 outputted concepts. Contrary to previous competitions, machine learning has this time outperformed standard dictionary-based approaches. Thanks to BioCreative IV, we were able to design a complete workflow for curation: given a gene name and a full text, this system is able to select evidence sentences for curation and to deliver highly relevant GO concepts. Contrary to previous competitions, machine learning this time outperformed dictionary-based systems. Observed performances are sufficient for being used in a real semiautomatic curation workflow. GOCat is available at http://eagl.unige.ch/GOCat/.


Via burkesquires
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Current Issues in Computational Biology and Bioinformatics

Google Tech Talks August 26, 2008 ABSTRACT A brief overview of bioinformatics computational problem landscape followed by a detailed look at one of the areas...
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Bioinformatics Software - SEQwiki

Bioinformatics Software - SEQwiki | Computational Biology | Scoop.it

Via Chris Upton + helpers
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Chris Upton + helpers's curator insight, January 30, 2013 1:20 PM

Always worth repeating....

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Bioinformatics Career Overview

A brief overview of Bioinformatics career opportunities brought to you by the University of South Dakota Computer Science Department.
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Rescooped by Kasia Chyżyńska from Bioinformatics Software: Sequence Analysis
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The digital toolbox: A new section of Nature examines the software and websites that make research easier

The digital toolbox: A new section of Nature examines the software and websites that make research easier | Computational Biology | Scoop.it
A new section of Nature examines the software and websites that make research easier.

Via Mel Melendrez-Vallard
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nucleotides · genome assembler benchmarking

continuous, objective and reproducible evaluation of genome assemblers using docker containers (Continuous, objective and reproducible evaluation of genome assemblers using @docker containers http://t.co/6hgzp7f7s5...
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Rescooped by Kasia Chyżyńska from SynBioFromLeukipposInstitute
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ROSALIND: an addictive bioinformatics learning site | Byte Size Biology

ROSALIND: an addictive bioinformatics learning site | Byte Size Biology | Computational Biology | Scoop.it

OOoh - DIY bioinformatics - this looks like a great teaching and learning resource!

 

"Mission statement: We hope that Rosalind will inspire a new generation of bioinformatics students by attracting biologists who want to develop vital programming skills at their own pace in a unique environment as well as programmers who have never been exposed to some of the stimulating computational problems generated by molecular biology."

http://rosalind.info/

 

http://mechanicalmooc.org/

A Gentle Introduction to Python could be useful...!


Via Mary Williams, David Gifford, Gerd Moe-Behrens
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Python For Bioinformatics and Your First Python for Bioinformatics Program

For more in-depth Python for Bioinformatics training visit: http://www.howtobioinformatics.com/pythonforBioinformatics Hi and welcome to Python for bioinform...
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Machine Learning for Computational Biology - Karsten Borgwardt - MLSS 2013 Tübingen

This is Karsten Borgwardt's talk on Machine Learning for Computational Biology, given at the Machine Learning Summer School 2013, held at the Max Planck Inst...
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