Open Source Python Bio-Informatics Software - Page 7

Tuque includes 4 programs: tuqueIndex to prepare Bowtie indexes that include spliced sequences tuqueMap to map reads using the prepared indices tuqueSplice to find splice junctions from the reads tuqueCount to count the reads mapping within annotated sequence intervals

Stochastic simulation model of poliovirus Sabin-to-Mahoney genetic state transition (C++ code). Models genotypes, virus populations, and quasispecies cloud. Simulates replication error and copy-choice recombination. Various parameters guiding the model are user-specified. Python code post-processes simulation output to produce report files.

UPDATE: LATEST VERSION AT http://git.durrantlab.com//jdurrant/wisp Allostery can occur by way of subtle cooperation among protein residues (e.g., amino acids) even in the absence of large conformational shifts. Dynamical network analysis has been used to model this cooperation, helping to computationally explain how binding to an allosteric site can impact the behavior of a primary site often many angstroms away. Traditionally, computational efforts have focused on the most optimal path of correlated motions leading from the allosteric to the primary active site. We present a program called Weighted Implementation of Suboptimal Paths (WISP) capable of rapidly identifying additional suboptimal pathways that may also play important roles in the transmission of allosteric signals. Aside from providing signal redundancy, suboptimal paths traverse residues that, if disrupted through pharmacological or mutational means, could modulate the allosteric regulation of important drug targets.

Wattos is a collection of mostly Java programs for Structural Biology and NMR Spectroscopy. It's programs analyze, annotate, parse, archive, and disseminate experimental NMR data deposited by authors world wide into the PDB and BMRB.

Sharing lists of molecular structures with associated chemical properties is a common task in computer-aided drug design and medicinal chemistry. WebChem Viewer is a simple, free, open-source program that generates HTML-formatted output that can be viewed in any modern web browser, on any operating system (including mobile), without requiring the installation of additional software. The output can also be easily incorporated into existing web pages. WebChem Viewer is released under the FreeBSD license. It was created by Jacob Durrant, a post-doc in the lab of Rommie E. Amaro.

python3 version of bibus https://sourceforge.net/projects/bibus-biblio/ It is nothing more than "it works on Debian testing (bookworm) AMD64. "

--UPDATE-- New Version is now integrated in the official PyMOL plugin repository! --UPDATE-- The BNI (Beyond Normal Interaction)- Tools is a plug in for the PyMOL molecular visualization system which adds additional functionalities and presets to the PyMOL GUI and also adds useful extended commands.

A lightweight python LIMS system

This script can convert raw diffraction images to JPEG files. Support ADSC, MarCCD, Mar345, RAXIS and PILATUS, and can be run on Windows, Linux and Mac OS X.

This is a pure Python CGI-based implementation of a taxonomically intelligent species search engine. It searches biological databases for a taxonomic name. The search is done "on the fly" using web services (SOAP/XML) or URL API's.

Metaproteomic analysis allows studying the interplay of organisms or functional groups and has become increasingly popular also for diagnostic purposes. However, difficulties arise due to the high sequence similarity between related organisms. Further, the state of conservation of proteins between species can be correlated with their expression level which can lead to significant bias in results and interpretation. These challenges are similar but not identical to the challenges arising in the analysis of metagenomic samples and require specific solutions. pipasic (peptide intensity-weighted proteome abundance similarity correction) is a tool which corrects identification and spectral counting based quantification results using peptide similarity estimation and expression level weighting within a non-negative lasso framework. pipasic has distinct advantages over approaches only regarding unique peptides or aggregating results to the lowest common ancestor.

pybrn is a Python package for the analysis of biochemical reaction networks. It provides basic model handling capabilities, import from SBML, analysis of conservation relations, steady state computation and model simulation.

RefineHMM refines an original hidden Markov model (HMM) to find an optimal fit against the evolutionary group that the HMM models, and it does this using through iterative database searches and incremental subsequent adaptation of the seed set.

Create, check, annotate, merge, diff, split SBML (System Biology Markup Lanugage) documents. The latest version of semanticSBML is webbased with a RESTful interface.

Update - SRST2 Now Available ------ 25 Sep, 2013 This project has now been replaced by SRST2 - Short Read Sequence Typing for Bacterial Pathogens, available at http://katholt.github.io/srst2/ The new SRST2 program does gene typing as well as MLST (e.g. typing resistance genes, virulence genes, etc). SRST2 is faster and more accurate than the old SRST, using bowtie2 to achieve local alignments (no need for flanking sequences) and a brand new scoring system.

tigreBrowser is a web-based browser for ranking results from R/Bioconductor package tigre and similar tools. It allows easy viewing, sorting and filtering of visualisations of models produced by tigre.

xPyder is a PyMOL plugin to analyze and visualize on the 3D structure dynamical cross-correlation matrices (DCCM), linear mutual information (LMI), communication propensities (CP), intra- and inter-molecular interactions (e.g. PSN), and more, to produce highly customizable publication-quality images. xPyder identifies networks (using concepts from graph theory, such as hubs and shortest path searching), compares matrices and focuses the analysis on relevant information by filtering the data using a modular, user-expandable plugin system that takes advantage of structural and dynamical information, contributing to bridge the gap between dynamical and mechanical properties at the molecular level.

ABE is a small, fast and convenient program for visualizing and modeling experimental bioassay data. The data can be modeled using either polynomials or a more specific four-parameter model based upon the standard, sigmoidal dose-response curve.

ADDA is a software package for finding domains in protein sequences. ADDA has moved to github (https://github.com/AndreasHeger/adda)

This project is A Mitochondrial OxydoReduction Simulation System. It consists of two linked projects: a program for displaying and analysing large biomolecular systems (Floral) and a multi-agent simulator for biomolecular oxydoreduction systems (AMORSS).

This software has moved to http://www.poissonboltzmann.org/.

Affymetrix GeneChip Operating Software (GCOS) is used to control Affymetrix Microarray scanners and fluidic stations. Using the DCOM API, this project provides programmatic scripting of GCOS using Python.

In Systems Biology models are created in various formats (Matlab, Java, C/C++, Python, ...). "Annotate Your Model" will help you to link your model to biological web resources by creating a CSV file containing MIRIAM annotations.

This is the backend source code of the Atlas2-Cloud pipeline on Amazon which starts and terminates worker nodes, runs analysis and monitors worker instances. It is PRIMARILY meant to be used through Amazon Web Services (AWS) management console by looking for the public Atlas2-Cloud machine image. Alternatively, the code can also be used for running the pipeline from your computer. By installing this software on your computer you will be setting up your computer to act as the head node which would then run the pipeline from your computer.

A collection of bioinformatics-related software created by members of Cancer Research UK (possibly among others).