:: DESCRIPTION
Bio C# contains classes for handling fasta IO, Blast-search (using an own algorithm), local and global alignments, quality sequence IO, statistics (Mann-Whitney, Poisson Distribution), distribution of features along chromosomes, SNP-identification, gene expression statistics, 454-sequence handling, microsatellite search and basic sequence statistics
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
QUT.Bio focuses on tools for bioinformatics and computational biology; new approaches to visualize sequences and the relationships between them—through SilverMap and SilverGene; and methods for promoter prediction, pattern description languages, and mash-ups.
:: DEVELOPER
QUT Institute of Health and Biomedical Innovation and the Queensland Facility for Advanced Bioinformatics
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: 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)
:: DESCRIPTION
pygr is a bioinformatics toolkit for sequence analysis and comparative genomics. pygr is highly scalable (e.g. one can easily query multi-genome alignments) and easy to use
Pygr is open source software to develop graph database interfaces for the popular Python language to make it easy to do powerful sequence and comparative genomics analyses, even with extremely large multi-genome data sets. pygr includes:
::DEVELOPER
Chris Lee, Dept. of Chemistry & Biochemistry,UCLA
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
PAICE (Pathway Analysis and Integrated Coloring of Experiments) is a rapid bioinformatics pathway visualization tool for KEGG-compatible accessions derived from Illumina Solexa next-gen and Affymetrix datasets. It colors KEGG pathways while appreciating detection-calls and duplicate gene copies.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformation. 2012;8(6):287-9. doi: 10.6026/97320630008287. Epub 2012 Mar 31.
MAPT and PAICE: Tools for time series and single time point transcriptionist visualization and knowledge discovery.
Hosseini P, Tremblay A, Matthews BF, Alkharouf NW.
:: DESCRIPTION
biowep is a web based client application that allows for the selection and execution of a set of predefined workflows. The system is available on-line. Biowep architecture includes a Workflow Manager, a User Interface and a Workflow Executor.
::DEVELOPER
Bioinformatics group, National Cancer Research Institute of Genoa
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2007 Mar 8;8 Suppl 1:S19.
Biowep: a workflow enactment portal for bioinformatics applications.
Romano P, Bartocci E, Bertolini G, De Paoli F, Marra D, Mauri G, Merelli E, Milanesi L.
:: DESCRIPTION
Ergatis is a web-based utility that is used to create, run, and monitor reusable computational analysis pipelines. It contains pre-built components for common bioinformatics analysis tasks. These components can be arranged graphically to form highly-configurable pipelines. Each analysis component supports multiple output formats, including the Bioinformatic Sequence Markup Language (BSML). The current implementation includes support for data loading into project databases following the CHADO schema, a highly normalized, community-supported schema for storage of biological annotation data.
::DEVELOPER
The Institute for Genome Sciences (IGS)
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Orvis J, Crabtree J, Galens K, Gussman A, Inman JM, Lee E, Nampally S, Riley D, Sundaram JP, Felix V, Whitty B, Mahurkar A, Wortman J, White O, Angiuoli SV.
Ergatis: A web interface and scalable software system for bioinformatics workflows.
Bioinformatics. 2010 Jun 15;26(12).
:: DESCRIPTION
Scripts and workflows written by NEBC members for analysis and standard tasks in bioinformatics.
::DEVELOPER
NERC Environmental Bioinformatics Centre.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
The BioC++ project provides an accessible and comprehensive framework of C/C++ tools and libraries for computational biology.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
BioDB-Loader toolkit loads several bioinformatics databases into Lisp for facile processin. BioDB-Loader contains utilities for loading flatfiles from the Swiss-Prot, Prosite, Enzyme, EcoCyc, and MetaCyc databases.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
