:: DESCRIPTION
JavaCycO is Java library for connecting to BioCyc Pathway Geneome Databases (PGDBs).
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
PathwayAccess: CellDesigner Plugins for Pathway Databases
John L. Van Hemert; Julie A. Dickerson
Bioinformatics 2010; doi: 10.1093/bioinformatics/btq423
:: DESCRIPTION
Bio-Formats is a standalone Java library for reading and writing life sciences image file formats. It is capable of parsing both pixels and metadata for a large number of formats, as well as writing to several formats. See the table below for a complete list (click the headers to sort, and format names to see all information).
Bio-Formats’s primary purpose is to convert proprietary microscopy data into an open standard called the OME data model, particularly into the OME-TIFF file format.
::DEVELOPER
development teams at The Open Microscopy Environment,
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:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
Compomics-utilities is an open-source support library for computational proteomics. The library contains a broad set of features required for reading, parsing, and analyzing proteomics data. compomics-utilities is already used by a long list of existing software, ensuring library stability and continued support and development.
::DEVELOPER
The Proteomics Unit at the University of Bergen (PROBE)
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Barsnes et al:
compomics-utilities: an open-source Java library for computational proteomics.
BMC Bioinformatics. 2011 Mar 8;12(1):70.
:: DESCRIPTION
Jannovar is a stand-alone Java application as well as a Java library designed to be used in larger software frameworks for exome analysis. Jannovar uses an interval tree to identify all transcripts affected by a given variant, and provides HGVS-compliant annotations for both for variants affecting coding sequences and splice junctions as well as UTR sequences and non-coding RNA transcripts. Jannovar can also perform family-based pedigree analysis with VCF files with data from members of a family segregating a Mendelian disorder. Using a desktop computer, Jannovar requires a few seconds to annotate a typical VCF file with exome data.
::DEVELOPER
The Computational Biology @ Charité Berlin
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Hum Mutat. 2014 May;35(5):548-55. doi: 10.1002/humu.22531. Epub 2014 Apr 9.
Jannovar: a java library for exome annotation.
Jäger M1, Wang K, Bauer S, Smedley D, Krawitz P, Robinson PN.
:: DESCRIPTION
mzQuantML is an XML-based format that captures extensive information from quantitative proteomics experiments.The mzqLibrary (mzqLibrary/mzqViewer) project intends to develop a set of easy-to-use post-processing APIs/applications to facilitate utilizing the standard in the field.
::DEVELOPER
:: SCREENSHOTS
n/a
:: REQUIREMENTS
:: MORE INFORMATION
Citation:
The mzqLibrary – An open source Java library supporting the HUPO-PSI quantitative proteomics standard.
Qi D, Zhang H, Fan J, Perkins S, Pisconti A, Simpson DM, Bessant C, Hubbard S, Jones AR.
Proteomics. 2015 Sep;15(18):3152-62. doi: 10.1002/pmic.201400535.
:: DESCRIPTION
ValWorkBench consists of a collection of measures for validation of clustering solutions and algorithms. It has external measures, as the Adjusted Rand index, and internal measures as Figure of Merit, Gap Statistics, Within Cluster Sum Square, Consensus Clustering and more.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
ValWorkBench: an open source Java library for cluster validation, with applications to microarray data analysis.
Giancarlo R, Scaturro D, Utro F.
Comput Methods Programs Biomed. 2015 Feb;118(2):207-17. doi: 10.1016/j.cmpb.2014.12.004.
:: DESCRIPTION
JSBML is a free, open-source, pure-Java library for working with SBML. It emulates libSBML’s API, with more Java idioms and without native object code.
JSBML is the library for reading, writing, and manipulating SBML files and data streams. It is an alternative to the mixed Java/native code-based interface provided in libSBML.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
JSBML 1.0: providing a smorgasbord of options to encode systems biology models.
Rodriguez N, Thomas A, Watanabe L, Vazirabad IY, Kofia V, Gómez HF, Mittag F, Matthes J, Rudolph J, Wrzodek F, Netz E, Diamantikos A, Eichner J, Keller R, Wrzodek C, Fröhlich S, Lewis NE, Myers CJ, Le Novère N, Palsson BØ, Hucka M, Dräger A.
Bioinformatics. 2015 Jun 16. pii: btv341
Bioinformatics. 2011 Aug 1;27(15):2167-8. doi: 10.1093/bioinformatics/btr361. Epub 2011 Jun 22.
JSBML: a flexible Java library for working with SBML.
Dräger A, Rodriguez N, Dumousseau M, Dörr A, Wrzodek C, Le Novère N, Zell A, Hucka M.
:: DESCRIPTION
Paxtools is a Java library specially designed for accessing and manipulating data in BioPAX format. The Paxtools Java programming library for BioPAX has been developed to help software developers readily support the import, export and validation of BioPAX-formatted data for various uses in their software . Using Paxtools, a range of BioPAX-compatible software has been developed, including browsers, visualizers, querying engines, editors and converters
PaxtoolsR provides a set of R functions for interacting with BioPAX OWL files using Paxtools and the querying Pathway Commons (PC) molecular interaction database that are hosted by the Computational Biology Center at Memorial Sloan-Kettering Cancer Center (MSKCC).
::DEVELOPER
Computational Biology Center at MSKCC
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
PaxtoolsR: Pathway Analysis in R Using Pathway Commons.
Luna A, Babur Ö, Aksoy BA, Demir E, Sander C.
Bioinformatics. 2015 Dec 18. pii: btv733.
Demir et al.
The BioPAX community standard for pathway data sharing
Nature Biotechnology 28 , 935–942 (2010) doi:10.1038/nbt.1666
:: DESCRIPTION
PAL (Phylogenetic Analysis Library) project is a collaborative effort to provide a high quality Java library for use in molecular evolution and phylogenetics. Updates of PAL are released in regular intervals. At present (version 1.4) PAL consists of approximately 200 public classes/interfaces in 16 packages with a total of more than 35,000 lines of Java code.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Drummond, A., and K. Strimmer. 2001.
PAL: An object-oriented programming library for molecular evolution and phylogenetics.
Bioinformatics 17: 662-663.
:: DESCRIPTION
CDK (The Chemistry Development Kit) is a Java library for structural chemo- and bioinformatics.The CDK provides methods for many common tasks in molecular informatics, including 2D and 3D rendering of chemical structures, I/O routines, SMILES parsing and generation, ring searches, isomorphism checking, structure diagram generation, etc.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
“The Chemistry Development Kit (CDK): An Open-Source Java Library for Chemo- and Bioinformatics“.
Steinbeck C., Han Y., Kuhn S., Horlacher O., Luttmann E., Willighagen E.L.,
J. Chem. Inf. Comput. Sci. 2003 Mar-Apr; 43(2):493-500 (DOI: 10.1021/ci025584y)
“Recent Developments of the Chemistry Development Kit (CDK) – An Open-Source Java Library for Chemo- and Bioinformatics“.
Steinbeck C., Hoppe C., Kuhn S., Floris M., Guha R., Willighagen E.L.,
Curr. Pharm. Des. 2006; 12(17):2111-2120 (DOI: 10.2174/138161206777585274)
