Bio-Informatics
Showing page 1 of 15.
-
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.
683 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/>.
161 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.
92 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.
129 weekly downloads -
MassMatrix Downloads MassMatrix downloads for PC version and software tools.
379 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.
267 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
83 weekly downloads -
STochastic Engine for Pathway Simulation Stochastic simulator for signaling pathways occuring in biological cells. Handles reaction-diffusion processes in 3D tetrahedral meshes.
35 weekly downloads -
SBW (Systems Biology Workbench) Framework for Systems Biology
52 weekly downloads -
PyCIFRW Python module for manipulation of Crystallographic Information Framework (CIF) files
176 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.
32 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.
71 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...
32 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.
127 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.
42 weekly downloads -
CONTIGuator CONTIGuator is a Python script for Linux environments whose purpose is to speed-up the bacterial genome assembly process and to obtain a first insight of the genome structure using the well-known artemis comparison tool (ACT).
18 weekly downloads -
PyRx - Virtual Screening Tool Virtual Screening software for Computational Drug Discovery
71 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.
14 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.
54 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.
47 weekly downloads -
LoFreq Sensitive variant-calling from sequencing data
23 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.
37 weekly downloads -
simuPOP A general-purpose individual-based forward-time population genetics simulation environment
37 weekly downloads -
QUAST Quality Assessment Tool for Genome Assemblies
36 weekly downloads -
Galileo: a Distributed Genetic Algorithm Galileo is a library for developing custom distributed genetic algorithms developed in Python. It provides a robust set of objects that can be used directly or as the basis of derived objects. Its modularity makes it easy to extend the functionality. The
19 weekly downloads
