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Anatomy of BioJS, an open source community for the life sciences.

Yachdav G, Goldberg T, Wilzbach S, Dao D, Shih I, Choudhary S, Crouch S, Franz M, García A, García LJ, Grüning BA, Inupakutika D, Sillitoe I, Thanki AS, Vieira B, Villaveces JM, Schneider MV, Lewis S, Pettifer S, Rost B, Corpas M - Elife (2015)

Bottom Line: BioJS is an open source software project that develops visualization tools for different types of biological data.Here we report on the factors that influenced the growth of the BioJS user and developer community, and outline our strategy for building on this growth.The lessons we have learned on BioJS may also be relevant to other open source software projects.

View Article: PubMed Central - PubMed

Affiliation: Bioinformatik, Biosof LLC, Garching, Germany.

ABSTRACT
BioJS is an open source software project that develops visualization tools for different types of biological data. Here we report on the factors that influenced the growth of the BioJS user and developer community, and outline our strategy for building on this growth. The lessons we have learned on BioJS may also be relevant to other open source software projects.

No MeSH data available.


Examples of BioJS tools.Tree Viewer (visualization of phylogeny data in a tree-like graph); MSA Viewer (visualization and analysis of multiple sequence alignments); Proteome (multilevel visualization of proteomes in UniProt; The UniProt Consortium, 2015); 3D structures (visualization of protein structures); Dot-bracket (visualization of RNA secondary structures); Muts-needle plot (presentation of mutation distribution across protein sequences). Protein Feature Viewer (visualization of position-based annotations in protein sequences); Plasmids (visualization of DNA plasmids); Pathway visualization (visualization of data from Pathway Commons; Cerami et al., 2011). Note that all visualization tools are native to the browser and do not require any specialized software (such as Adobe flash, Java Virtual Machine or Microsoft Silverlight) to be installed or loaded.DOI:http://dx.doi.org/10.7554/eLife.07009.002
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fig1: Examples of BioJS tools.Tree Viewer (visualization of phylogeny data in a tree-like graph); MSA Viewer (visualization and analysis of multiple sequence alignments); Proteome (multilevel visualization of proteomes in UniProt; The UniProt Consortium, 2015); 3D structures (visualization of protein structures); Dot-bracket (visualization of RNA secondary structures); Muts-needle plot (presentation of mutation distribution across protein sequences). Protein Feature Viewer (visualization of position-based annotations in protein sequences); Plasmids (visualization of DNA plasmids); Pathway visualization (visualization of data from Pathway Commons; Cerami et al., 2011). Note that all visualization tools are native to the browser and do not require any specialized software (such as Adobe flash, Java Virtual Machine or Microsoft Silverlight) to be installed or loaded.DOI:http://dx.doi.org/10.7554/eLife.07009.002

Mentions: BioJavaScript (BioJS; http://biojs.net/) was set up to meet a need for an open source library of reusable components to visualize and analyse biological data on the web (Figure 1; Corpas et al., 2014). These components are discrete modules that can be reused, extended and combined to meet a particular visualization need. Unlike proprietary (or closed-source) systems, which are typically distributed as ‘executable’ files under restrictive licenses, open source software projects make their source code freely available under a permissive license (Millington, 2012; Balch, et al., 2015). This allows other users to modify, extend and re-distribute the software with few restrictions and at no cost to other users.10.7554/eLife.07009.002Figure 1.Examples of BioJS tools.


Anatomy of BioJS, an open source community for the life sciences.

Yachdav G, Goldberg T, Wilzbach S, Dao D, Shih I, Choudhary S, Crouch S, Franz M, García A, García LJ, Grüning BA, Inupakutika D, Sillitoe I, Thanki AS, Vieira B, Villaveces JM, Schneider MV, Lewis S, Pettifer S, Rost B, Corpas M - Elife (2015)

Examples of BioJS tools.Tree Viewer (visualization of phylogeny data in a tree-like graph); MSA Viewer (visualization and analysis of multiple sequence alignments); Proteome (multilevel visualization of proteomes in UniProt; The UniProt Consortium, 2015); 3D structures (visualization of protein structures); Dot-bracket (visualization of RNA secondary structures); Muts-needle plot (presentation of mutation distribution across protein sequences). Protein Feature Viewer (visualization of position-based annotations in protein sequences); Plasmids (visualization of DNA plasmids); Pathway visualization (visualization of data from Pathway Commons; Cerami et al., 2011). Note that all visualization tools are native to the browser and do not require any specialized software (such as Adobe flash, Java Virtual Machine or Microsoft Silverlight) to be installed or loaded.DOI:http://dx.doi.org/10.7554/eLife.07009.002
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4495654&req=5

fig1: Examples of BioJS tools.Tree Viewer (visualization of phylogeny data in a tree-like graph); MSA Viewer (visualization and analysis of multiple sequence alignments); Proteome (multilevel visualization of proteomes in UniProt; The UniProt Consortium, 2015); 3D structures (visualization of protein structures); Dot-bracket (visualization of RNA secondary structures); Muts-needle plot (presentation of mutation distribution across protein sequences). Protein Feature Viewer (visualization of position-based annotations in protein sequences); Plasmids (visualization of DNA plasmids); Pathway visualization (visualization of data from Pathway Commons; Cerami et al., 2011). Note that all visualization tools are native to the browser and do not require any specialized software (such as Adobe flash, Java Virtual Machine or Microsoft Silverlight) to be installed or loaded.DOI:http://dx.doi.org/10.7554/eLife.07009.002
Mentions: BioJavaScript (BioJS; http://biojs.net/) was set up to meet a need for an open source library of reusable components to visualize and analyse biological data on the web (Figure 1; Corpas et al., 2014). These components are discrete modules that can be reused, extended and combined to meet a particular visualization need. Unlike proprietary (or closed-source) systems, which are typically distributed as ‘executable’ files under restrictive licenses, open source software projects make their source code freely available under a permissive license (Millington, 2012; Balch, et al., 2015). This allows other users to modify, extend and re-distribute the software with few restrictions and at no cost to other users.10.7554/eLife.07009.002Figure 1.Examples of BioJS tools.

Bottom Line: BioJS is an open source software project that develops visualization tools for different types of biological data.Here we report on the factors that influenced the growth of the BioJS user and developer community, and outline our strategy for building on this growth.The lessons we have learned on BioJS may also be relevant to other open source software projects.

View Article: PubMed Central - PubMed

Affiliation: Bioinformatik, Biosof LLC, Garching, Germany.

ABSTRACT
BioJS is an open source software project that develops visualization tools for different types of biological data. Here we report on the factors that influenced the growth of the BioJS user and developer community, and outline our strategy for building on this growth. The lessons we have learned on BioJS may also be relevant to other open source software projects.

No MeSH data available.