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Bench Marks for Computational Biology #
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Biology

Bench Marks for Computational Biology #

Computational biologist creating a path for new dynamic young researches and guiding the experimentalist to overcome the limits of wet lab problems through computational predictions with intensive heuristic analyzes and setting up the benchmarks. They improved a lot on the basis of credibility on computational algorithms and the bioinformatics software’s. Scientist accomplished that task through the collective effort from worldwide computational biologist on versatile topics to simulate the central dogma of molecular biology.

The forums were organized such as The Assemblathon (DNA sequence assembly), CAGI (Genome Interpretation for phenotype variations), RNA-Puzzles (RNA 3D structure modeling), and CASP (Protein 3D structure modeling). Moreover, the reorganization for the computational biologist was initiated through Noble Award 2013 – Chemistry to Martin Karplus, Michael Levitt and Arieh Warshel for their “Multi scale methods for complex systems”.

  • Note: Sentence were taken from the respective websites.

CASP - Critical Assessment of Structure Prediction #

Web Site : http://predictioncenter.org/

CASP goal is to help advance the methods of identifying protein structure from sequence. The Center has been organized to provide the means of objective testing of these methods via the process of blind prediction. The Critical Assessment of protein Structure Prediction (CASP) experiments aim at establishing the current state of the art in protein structure prediction, identifying what progress has been made, and highlighting where future effort may be most productively focused. Till now 12 meetings held (CASP1 (1994) to CASP (2014)).

Noble Award 2013 : Martin Karplus, Michael Levitt and Arieh Warshel

CAGI – Critical Assessment of Genome Interpretation #

Web Site : https://genomeinterpretation.org/

The Critical Assessment of Genome Interpretation (CAGI, \'kā-jē) is a community experiment to objectively assess computational methods for predicting the phenotypic impacts of genomic variation. Till now, there were three meetings organized. (Started From 2010, 2011 and 2012-13. The next one will be in 2015.

The Assemblathon #

Web Site: http://assemblathon.org/

The Assemblathon is a collaborative, recurring effort to spur improvements in computational methods for genome assembly. Teams use their own software to assemble one or more genomes that the organizers of the Assemblathon make available (see the rules for more details). All participants have the same amount of time to try to assemble the genomes, and then the organizers evaluate each group's efforts. Till now there was two meetings (2011 and 2013)

RNA-Puzzles #

Web Site : http://paradise-ibmc.u-strasbg.fr/rnapuzzles

The goals are to assess the leading edge of RNA structure prediction techniques; compare existing methods and tools; and evaluate their relative strengths, weaknesses, and limitations in terms of sequence length and structural complexity. The results should give potential users insight into the suitability of available methods for different applications and facilitate efforts in the RNA structure prediction community in ongoing efforts to improve prediction tools. We also report the creation of an automated evaluation pipeline to facilitate the analysis of future RNA structure prediction exercises. Started at 2012.

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