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Biology (58)

Antidote is an open source implementation of the IEEE 11073-20601 standard. It also contains the implementation of a D-Bus based 11073 manager service.

Arvados enables you to quickly begin using cloud computing resources in your data science work. It allows you to track your methods and datasets, share them securely, and easily re-run analyses.

BamTools provides both a programmer's API and an end-user's toolkit for handling genome alignment files in the BAM and SAM format. A BAM file (.bam) is the binary version of a SAM file. A SAM file (.sam) is a tab-delimited text file that contains sequence alignment data.

A python toolkit providing best-practice pipelines for fully automated high throughput RNA sequencing analysis. It can work with BWA, .bam or .fastq files.

BioMail automates searching for recent scientific papers in the PubMed Medline database, and can periodically run a customized Medline search and send all recent matching articles to the user's e-mail address. You can save search patterns: no more remembering which search was good and which wasn't. It is intended for medical researchers, biologists, and anyone who wants to know the latest information about a disease or a biological phenomenon. It is also useful for users who have email address but slow or sporadic Web access; they can set up searches and have them emailed to an address instead of having to surf the Web themselves for the information.

Bioinformatics Template Library
This library focuses on the data structures and algorithms used in bioinformatics and molecular modelling, following closely the approach of the Standard Template Library (STL) to implement efficient generic programming modules using compile time mechanisms. Although the BTL was designed with biomolecular applications in mind it contains classes of more general utility: for instance, the Matrix class could be used for matrix algebra in many contexts.

Biskit is a python library for structural bioinformatics research. It simplifies the analysis of macromolecular structures, protein complexes, and molecular dynamics trajectories and offers a platform for the rapid integration of external programs.

Blossoc is a linkage disequilibrium association mapping tool that attempts to build (perfect) genealogies for each site in the input, score these according to non-random clustering of affected individuals, and judge high-scoring areas as likely candidates for containing disease affecting variation. Building the local genealogy trees is based on a number of heuristics that are not guaranteed to build true trees, but have the advantage over more sophisticated methods of being extremely fast. Blossoc can therefore handle much larger data sets than more sophisticated tools, but at the cost of sacrificing some accuracy.

Bmrblib is a Python API abstracting the Biological Magnetic Resonance Data Bank (BioMagResBank or BMRB) NMR-STAR format ( It allows the writing of NMR-STAR files for BMRB data deposition and the reading and easy extraction of data from files residing in the BMRB data bank, all without knowledge of the Self-Defining Text Archive and Retrieval (STAR) format.

A generic and fairly complete cellular automata simulation engine. CAGE is a fairy generic and complete cellular automaton simulation engine in Python. It supports both 1D and 2D automata, a variety of prepackaged rules, and the concept of "agents" which can move about independently on the map for implementing agent behavior. CAGE comes with numerous examples of fully-functional CA systems, including Conway's Game of Life, Langton's self-reproducing automaton, Langton's "vants," and 1D automata rule explorers. It also comes with simple displayers (including a curses interface for 2D automata). Also included is a unique implementation of a finite state machine (

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