New Bioinformatics for Linux
STEPS is a package for exact stochastic simulation of reaction-diffusion systems in arbitrarily complex 3D geometries. Our core simulation algorithm is an implementation of Gillespie's SSA, extended to deal with diffusion of molecules over the elements of...
NEO (Neural Ensemble Objects) and is a project to provide a common set of base classes to be used in neural data analysis, with the aim of getting OpenElectrophy, NeuroTools and maybe other projects with similar goals more close together.Two major...
OpenElectrophy is a framework to facilitate manipulation, storage and analysis of electrophysiological data. It can import data from many different file formats and store them in a single SQL-type database.Analysis tools included in OpenELectrophy are...
PEAT is a suite of programs for capturing, predicting and analyzing biophysical characteristics of proteins.See http://enzyme.ucd.ie/PEAT for documentation, instructions, screenshots etc.Requirements:cursor-pointer" onclick="spovl3hide();"> System...
Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome.The software implements two algorithms, bwa-short and BWA-SW. The former works for query...
SSuMMo is a library of functions designed around iteratively using hmmer to assign sequences to taxa. Results are highly annotated trees showing species / genus distribution within that community.Programs included with the source code include tools...
goby is a Python API for reading binary data files created using the Goby next-gen data management framework.Normally, this directory comes as part of the complete Goby package, available from: http://goby.campagnelab.org/The complete package...
PySCeS is a project developed by the Triple-J Group for Molecular Cell Physiology in order to try model and understand the complex processes and systems which make up the living cell.Features:cursor-pointer" onclick="spovl3hide();"> Application...
Pysam is a Python module for reading and manipulating Samfiles. It's a lightweight wrapper of the samtools C-API.The quick start guide is here. More detailed documentation is available here.Questions and comments are very welcome and should be send...
TRMiner is a Python utility that aims at scientific data curators. It allows to rapidly prune large collections of scientific publications to sentences relevant for a given mining goal.This is achieved in two steps. First, texts are tranlated into...
