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ProStack - a platform for image processing and analysis
ProStack - a platform for image processing and analysis. It implements various image processing methods as separate modules, that can be joined in a complex image processing scenario by use of a graphical userinterface.
RPMs are available at https://build.opensuse.org/project/repositories/home:mackoel:compbio
APBSmem is a Java-based graphical userinterface for Poisson-Boltzmann electrostatics calculations at the membrane. APBS version 1.2.0 or later is required.
hr ("High Resolution") is a small command-line utility to calculate possible elemental compositions for a given mass. It allows to run calculations interactively, in batch mode, via the command line, or (using a webserver) via a web interface.
'isotope' is a small command-line utility to calculate the isotope pattern for a given chemical formula. It allows to run calculations interactively, in batch mode, via the command line, or (using a webserver) via a web interface.
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bruread is a program to read and display NMR data in the Bruker XWIN-NMR format. The program has a command-line interface and a graphic display based on gnuplot. - Note that this is only an NMR spectrum *viewer*, not a full-fledged data evaluation suite
Epidaurus is a collection of epigenetic datasets including transcription factor ChIP-seq, histone ChIP-seq, DNase-seq, FAIRE-seq, DNA methylation, etc. It also includes commonly used genome features (GC content, conservation) and RNA-seq. A user friendly interface has been developed to interrogate and visuzlize these datasets.
TinkerCell is a software for synthetic biology. The visual interface allows users to design networks using various biological "parts". Models can include modules and multiple cells. Users can program new functions using C or Python. www.tinkercell.
wEMBOSS is a Web interface for the EMBOSS software package for biological sequence analysis. Under wEMBOSS each user has a private workspace (UNIX home directory) on the server, where he can permanently store his data and organize them in projects.
The companion suite wrappers4EMBOSS allows to integrate under EMBOSS a number of popular bioinformatic software suites as BLAST, CLUSTAL and MRS.
The goal of PlaTypUS is to establish a unified Plasmodium whole genome analysis tool, that aligns short read sequences in an agreed upon manner, with many quality control steps, and calls both SNVs and CNVs in a community agreed standard way. We also seek to provide this analysis in a stand-alone graphic userinterface so that labs around the world can analyze their own whole genome sequencing data, rather than relying on outside institutes.
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The DeconSeq tool can be used to automatically detect and efficiently remove sequence contamination from genomic and metagenomic datasets. It is easily configurable and provides a user-friendly interface. More at http://deconseq.sourceforge.net
CoactivationMap is a graphic userinterface to browse through a map of functional co-activations of the human brain. Click on a region, and observe which other regions are likely to be connected
EMBOSS is a dynamic and comprehensive Open Source package for bioinformatics (DNA and protein sequence analysis, protein structure, phylogenetics, etc.). EMBOSS is written in C, also compatible with C++, and has a separate Java interface (Jemboss)
ProgPorts is an administrative and easy userinterface to hundreds of proteomics, molecular dynamics, and protein crystallography programs. It is a hybrid of the prog/setup system, developed at Johns Hopkins University, and GNU-Darwin ports system.
Bio-SPHERE aims to create a flexible, secure and multimodal biometric platform for applications that require biometrics. Bio-SPHERE is formed by a network of interacting nodes that interface with biometric hardware and offer biometric functions.
A toolbox for quantitative morphometric analysis of early development in spherical embryos, such as Xenopus laevis (African Clawed Frog). The toolbox is developed for Matlab 6.5 and higher and combines C-Mex code with Matlab functions.
Gnome-EMBOSS is an open-source application to help scientists handle DNA, RNA and protein sequences.
It uses Gnome/GTK for the userinterface and EMBOSS libraries for sequence handling routines. (See www.emboss.org for further info.)