Bio-Informatics
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Gwyddion A data visualization and processing tool for scanning probe miscroscopy (SPM, i.e. AFM, STM, MFM, SNOM/NSOM, ...) and profilometry, useful also for general image and 2D data analysis.
647 weekly downloads -
APBS APBS is a software package for the numerical solution of the Poisson-Boltzmann equation, a popular continuum model for describing electrostatic interactions between molecular solutes over a wide range of length scales. <http://www.poissonboltzmann.org/>.
135 weekly downloads -
BioImageXD BioImageXD - free open source software for analysis, processing and 3D rendering of multi dimensional, multi data channel, time series image data from microscopy and other sources.
90 weekly downloads -
PyCogent The PyCogent project is moving to GitHub. When completed, you will find us at http://github.com/pycogent/pycogent/. You can find the PyCogent website at http://www.pycogent.org.
119 weekly downloads -
The igraph library This is another library for creating and manipulating graphs. There is simply no other graph library out there which can handle graphs of the size the author is confronted with. Whenever possible igraph tries to be also user friendly and portable.
244 weekly downloads -
STochastic Engine for Pathway Simulation Stochastic simulator for signaling pathways occuring in biological cells. Handles reaction-diffusion processes in 3D tetrahedral meshes.
36 weekly downloads -
raxmlGUI A userfriendly graphical front-end for phylogenetic analyses using RAxML (Stamatakis, 2006). Please cite: Silvestro, Michalak (2012) - raxmlGUI: a graphical front-end for RAxML. Organisms Diversity and Evolution 12, 335-337. DOI: 10.1007/s13127-011-0056-0
57 weekly downloads -
SBW (Systems Biology Workbench) Framework for Systems Biology
46 weekly downloads -
Febrl Febrl (Freely Extensible Biomedical Record Linkage) does data standardisation (segmentation and cleaning) and probabilistic record linkage ("fuzzy" matching) of one or more files or data sources which do not share a unique record key or identifier.
29 weekly downloads -
PyCIFRW Python module for manipulation of Crystallographic Information Framework (CIF) files
122 weekly downloads -
TinkerCell : CAD for Synthetic Biology 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.
67 weekly downloads -
PyDSTool This is a sophisticated & integrated simulation and analysis environment for dynamical systems models of physical systems (ODEs, DAEs, maps, and hybrid systems). It supports symbolic math, optimization, continuation, data analysis, biological apps...
29 weekly downloads -
openModeller openModeller is a complete C++ framework for species potential distribution modelling. The project also includes a graphical user interface, a web service interface and an API for Python.
111 weekly downloads -
PyRx - Virtual Screening Tool Virtual Screening software for Computational Drug Discovery
70 weekly downloads -
PDB2PQR PDB2PQR is a Python software package that automates many of the common tasks of preparing structures for continuum electrostatics calculations, providing a platform-independent utility for converting protein files in PDB format to PQR format.
32 weekly downloads -
CBFlib CBFLIB is a library of ANSI-C functions providing a simple mechanism for accessing Crystallographic Binary Files (CBF files) and Image-supporting CIF (imgCIF) files. The CBFLIB API is loosely based on the CIFPARSE API for mmCIF files.
53 weekly downloads -
CONTRA Copy Number Analysis for Targeted Resequencing (CONTRA) is a tool for copy number variation (CNV) detection for targeted resequencing data such as those from whole-exome capture data.
45 weekly downloads -
LoFreq Sensitive variant-calling from sequencing data
23 weekly downloads -
QUAST Quality Assessment Tool for Genome Assemblies
40 weekly downloads -
QIIME The QIIME project has moved to GitHub. You can now find us at http://github.com/qiime/. As always, you can find the QIIME website at http://www.qiime.org.
9 weekly downloads -
CoNIFER Homepage for CoNIFER (Copy Number Inference From Exome Reads)
35 weekly downloads -
General Hidden Markov Model Library The General Hidden Markov Model Library (GHMM) is a C library with additional Python bindings implementing a wide range of types of Hidden Markov Models and algorithms: discrete, continous emissions, basic training, HMM clustering, HMM mixtures.
34 weekly downloads -
CBMPy Constraint Based Modelling in Python
29 weekly downloads -
xPyder PyMOL Plugin Analyze and visualize coupled residues and their networks in proteins
10 weekly downloads -
PBJelly Genome Upgrading using Long-Read Sequencing
13 weekly downloads
