:: DESCRIPTION
RMAExpress is a standalone GUI program for Windows (and Linux) to compute gene expression summary values for Affymetrix Genechip® data using the Robust Multichip Average expression summary and to carry out quality assessment using probe-level metrics.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
giflu is a small c++ program used to generate input files for Baesc from BioRad Luminex system output files.
::DEVELOPER
The Center for Computational Immunology
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
Chip2Spell aims to speed up the preparation of linkage data files passed on to the Alohomora software for data from the Affymetrix or Illumina assays. Chip2Spell gathers the information necessary to supplement the genotype data (such as the genetic map of the markers and the population-specific allele frequencies) from publicly available annoation files from Affymetrix and Illumina. The program formats the genotype data for input into the Alohomora program.
::DEVELOPER
Marie-Pierre Dubé’s Laboratory
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: MORE INFORMATION
:: DESCRIPTION
savvy is a CGI web app to generate high resolution print quality plasmid map using SVG.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
MOLGENIS ( MOLecular GENetics Information Systems) is an collaborative open source project on a mission to generate great software infrastructure for life science research. Each app in the MOLGENIS family comes with rich data management interface and plug-in integration of analysis tools in R, Java and web services. The MOLGENIS platform allows you to automatically generate rich database software to your specifications, including web user interfaces to manage and query your data, various database back ends to store your data, and programmatic interfaces to the R language and web services. You tell MOLGENIS what to generate using an data model and user interface model described in XML; at the push of a button MOLGENIS translates this model into SQL, Java and R program files. Also documentation is generated. While the standard generated MOLGENIS is sufficient for most data management needs, MOLGENIS also allows you to plug in handwritten software components that build on the auto-generated software platform.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
BMC Bioinformatics. 2010 Dec 21;11 Suppl 12:S12.
The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button.
Swertz MA, Dijkstra M, Adamusiak T, van der Velde JK, Kanterakis A, Roos ET, Lops J, Thorisson GA, Arends D, Byelas G, Muilu J, Brookes AJ, de Brock EO, Jansen RC, Parkinson H.
:: DESCRIPTION
SHiAT (Shannon Heterogeneity in Alignments Tool) provides an intuitive graphical interface for the simultaneous calculation of three measures of sitewise variation in DNA or RNA alignments. The Shannon Information index, Hamming distance and (1-consensus frequency) are all calculated and displayed in a series of graphical plots. Multiple alignments may be imported and compared, and a data view panel allows easy copy-and-pasting into external applications.
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:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
SBMLsqueezer generates kinetic equations for biochemical networks according to context of each reaction. When used as a plugin for CellDesigner it uses the information from the SBGN representation of all network components. In the stand-alone mode, SBMLsqueezer evaluates the Systems Biology Ontology (SBO) annotations to extract this information.
The rate laws that can be produced by SBMLsqueezer include several types of generalized mass action; detailed and generalized enzyme kinetics, various types of Hill equations, S- and H-systems, and additive models for gene regulation. User defined settings specify which equation to apply for any type of reaction and how to ensure unit consistency of the model. Equations can be created using contextual menus. All newly created parameters are equipped with the derived unit and annotated with SBO terms if available and meaningful textual names. MathML is inserted directly into the SBML file. LaTeX or text export of ordinary differential equations is provided.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
SBMLsqueezer: a CellDesigner plug-in to generate kinetic rate equations for biochemical networks.
Dräger A, Hassis N, Supper J, Schröder A, Zell A.
BMC Syst Biol. 2008 Apr 30;2:39. doi: 10.1186/1752-0509-2-39.
:: DESCRIPTION
ESPript (Easy Sequencing in Postscript) is a utility to generate a pretty PostScript output from aligned sequences.
ENDscript is an interface grouping eight types of Programs: BLAST; MULTALIN/ CLUSTALW; DSSP; CNS; ESPript; BOBSCRIPT/ MOLSCRIPT; DINO; PHYLODENDRON; PROFIT.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Gouet, P., Courcelle, E., Stuart, D.I. and Metoz, F. (1999).
ESPript: analysis of multiple sequence alignments in PostScript
Bioinformatics. 15 305-8
Nucleic Acids Res. 2003 Jul 1;31(13):3320-3.
ESPript/ENDscript: Extracting and rendering sequence and 3D information from atomic structures of proteins.
Gouet P, Robert X, Courcelle E.
:: DESCRIPTION
PRINSEQ (PReprocessing and INformation of SEQuence data.) is a tool that generates summary statistics of sequence and quality data and that is used to filter, reformat and trim next-generation sequence data. It is particular designed for 454/Roche data, but can also be used for other types of sequence data. PRINSEQ is available through a user-friendly web interface or as standalone version. The standalone version is primarily designed for data preprocessing and does not generate summary statistics in graphical form.
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:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Schmieder R and Edwards R
Quality control and preprocessing of metagenomic datasets.
Bioinformatics 2011, 27:863-864.
:: DESCRIPTION
OGDraw (OrganelleGenomeDraw) is a tool that enables the user to quickly generate high-quality graphical maps of circular DNA sequences. Though especially designed and optimized for the display of small organelle genomes like the chloroplast or mitochondrial genome, it is applicable to all circular DNA sequences. The input data can be provided as GenBank files or GenBank accession numbers.
::DEVELOPER
Max Planck Institute for Molecular Plant Physiology
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Nucleic Acids Res, 47 (W1), W59-W64 2019 Jul 2
OrganellarGenomeDRAW (OGDRAW) Version 1.3.1: Expanded Toolkit for the Graphical Visualization of Organellar Genomes
Stephan Greiner , Pascal Lehwark , Ralph Bock
Curr Genet. 2007 Nov;52(5-6):267-74. Epub 2007 Oct 24.
OrganellarGenomeDRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes.
Lohse M, Drechsel O, Bock R.
