Dataset Information

The GenABEL Project for statistical genomics.

ABSTRACT: Development of free/libre open source software is usually done by a community of people with an interest in the tool. For scientific software, however, this is less often the case. Most scientific software is written by only a few authors, often a student working on a thesis. Once the paper describing the tool has been published, the tool is no longer developed further and is left to its own device. Here we describe the broad, multidisciplinary community we formed around a set of tools for statistical genomics. The GenABEL project for statistical omics actively promotes open interdisciplinary development of statistical methodology and its implementation in efficient and user-friendly software under an open source licence. The software tools developed withing the project collectively make up the GenABEL suite, which currently consists of eleven tools. The open framework of the project actively encourages involvement of the community in all stages, from formulation of methodological ideas to application of software to specific data sets. A web forum is used to channel user questions and discussions, further promoting the use of the GenABEL suite. Developer discussions take place on a dedicated mailing list, and development is further supported by robust development practices including use of public version control, code review and continuous integration. Use of this open science model attracts contributions from users and developers outside the "core team", facilitating agile statistical omics methodology development and fast dissemination.

SUBMITTER: Karssen LC

PROVIDER: S-EPMC4916982 | biostudies-other | 2016

REPOSITORIES: biostudies-other

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The GenABEL Project for statistical genomics.

Karssen Lennart C LC van Duijn Cornelia M CM Aulchenko Yurii S YS

F1000Research 20160519

Development of free/libre open source software is usually done by a community of people with an interest in the tool. For scientific software, however, this is less often the case. Most scientific software is written by only a few authors, often a student working on a thesis. Once the paper describing the tool has been published, the tool is no longer developed further and is left to its own device. Here we describe the broad, multidisciplinary community we formed around a set of tools for stati ...[more]

PMID: 27347381

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Project description:Protein identification was carried out by searching against a joint Human + Yeast Swissprot database (Uniprot release 57.3 May 2009, 26885 entries), in order to increase statistical power of peptide identification, which was supplemented with porcine trypsin, and using SEQUEST algorithm (Bioworks 3.2 package, Thermo Finnigan). For SILAC, we used variable (methionine oxidation, lysine and arginine modification of +6 Da) and fixed modifications (cysteine carboxamidomethylation). Precursor mass tolerance was set to 2Da, fragment mass tolerance to 1.2Da and up to two missed cleavage sites for trypsin were allowed. The same collections of MS/MS spectra were also searched against inverted databases constructed from the same target databases. SEQUEST results were analyzed using the probability ratio method 22b, taking into account isoelectric points of peptides to improve peptide identification 9b. False discovery rates (FDR) of peptide identifications were calculated from the search results against the inverted databases using the refined method 9b. The combination of stable isotope labeling (SIL) with mass spectrometry (MS) allows comparison of the abundance of thousands of proteins in complex mixtures. However, interpretation of the large datasets generated by these techniques remains a challenge since appropriate statistical standards are lacking. Here we present the first generally applicable model that accurately explains the behavior of data obtained using current SIL approaches, including 18O, iTRAQ and SILAC labeling, and different MS instruments. The model decomposes the total technical variance into the spectral, peptide and protein variance components, and its general validity was demonstrated by confronting 48 experimental distributions against 18 different null hypotheses. In addition to its general applicability, the performance of the algorithm was similar or better than that of other existing methods. The model also provides a general framework to integrate quantitative information, allowing a comparative analysis of the results obtained from different SIL experiments. The model was applied to the global analysis of protein alterations induced by low H2O2 concentrations in yeast, demonstrating the increased statistical power that may be achieved by rigorous data integration. Our results highlight the importance of establishing an adequate and validated statistical framework for the analysis of high-throughput data. Except for TOF/TOF MS/MS files, protein identification was carried out by searching against a joint Human+YeastSwissprot database (Uniprot release 57.3 May 2009, 26885 entries), in order to increase statistical power of peptide identification, which was supplemented with porcine trypsin, and using SEQUEST algorithm (Bioworks 3.2 package, Thermo Finnigan). For 18O-labeled samples variable (methionine oxidation, lysine and arginine modification of +4 Da) and fixed modifications (cysteine carboxamidomethylation) were used. For iTRAQ, we allowed variable (methionine oxidation) and fixed modifications (cysteine carboxamidomethylation, lysine and N- terminal modification of +144.1020 Da). For SILAC, we used variable (methionine oxidation, lysine and arginine modification of +6 Da) and fixed modifications (cysteine carboxamidomethylation). Precursor mass tolerance was set to 2Da, fragment mass tolerance to 1.2Da and up to two missed cleavage sites for trypsin were allowed. The same collections of MS/MS spectra were also searched against inverted databases constructed from the same target databases. SEQUEST results were analyzed using the probability ratio method 22b, taking into account isoelectric points of peptides to improve peptide identification 9b. False discovery rates (FDR) of peptide identifications were calculated from the search results against the inverted databases using the refined method 9b. TOF/TOF MS/MS spectra were converted to MGF files by using the 4000 Series Explorer V.3.5.1 internal processor and the following parameters: mass range from precursor -20 Da to 60 Da, peak density of 50 peaks per 200 Da with S/N >1 and minimum area >1 with a maximum number of 100 peaks per precursor. These files were analyzed with the Mascot V2.2.06 search engine using the database and search conditions indicated above.

Dataset Information

The GenABEL Project for statistical genomics.

Publications

The GenABEL Project for statistical genomics.

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