228 projects tagged "Bioinformatics"

No download Website Updated 07 Dec 2010 BALL

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Pop 141.95
Vit 3.53

The Biochemical ALgorithms Library (BALL) is a framework for rapid application development in molecular modeling and structural bioinformatics. BALL provides an extensive set of data structures as well as classes for molecular mechanics, advanced solvation methods, comparison and analysis of protein structures, file import/export, NMR shift prediction, and visualization. Its extensibility results from an object-oriented and generic programming approach.

Download Website Updated 28 Oct 2011 BALLView

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Pop 61.25
Vit 6.59

BALLView is an extensible viewer for bio-molecular structures. It provides all standard models and offers rich functionality for molecular modeling and simulation, including molecular mechanics methods (AMBER, CHARMM, and MMFF94 force fields), continuum electrostatics methods employing a Finite-Difference Poisson Boltzmann solver, secondary structure calculation, molecular editing and docking. Since BALLView is based on BALL (the Biochemical ALgorithms Library), it is easily extensible on the level of C++ code. In addition, it provides a Python interface with Integrated Development Environment features to allow interactive rapid prototyping.

No download Website Updated 23 May 2004 BLAST on CD

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Pop 17.26
Vit 1.00

BLAST on CD is a live CD distribution based on DNAlinux that runs the NCBI BLAST server. It does not require installation and comes with the SARS and smallpox genomes.

Download Website Updated 01 Mar 2008 Babase

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Pop 54.31
Vit 1.00

Babase is a baboon data management system. It is designed to facilitate the retrieval, storage, maintenance, and analysis of the following broad data categories: group membership, social status (dominance rank), life events, sexual cycle events (including progeny), sexual cycle day-to-day status, dyadic social interactions, focal animal samples, and multi-party social interactions. Integration of other data is supported. Babase is designed for Web access.

Download Website Updated 05 Mar 2012 Basic Local Alignment Search Tool

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Pop 79.22
Vit 9.36

BLAST is a set of similarity search programs designed to explore all of the available sequence databases regardless of whether the query is protein or DNA. It uses a heuristic algorithm which seeks local as opposed to global alignments, and is therefore able to detect relationships among sequences which share only isolated regions of similarity. It can be run locally as a full executable, and can be used to run BLAST searches against private, local databases, or downloaded copies of the NCBI databases. It runs on Mac OS, Win32, LINUX, Solaris, IBM AIX, SGI, Compaq OSF, and HP- UX systems.

No download Website Updated 23 Feb 2011 Berkeley DB XML

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Pop 131.07
Vit 3.10

Berkeley DB XML is a native XML database engine for use within your product. Made available as a C++ library with language bindings for Java, Perl, Python, PHP, and Tcl, it integrates directly into your application (it is not a standalone database server). It provides XQuery access into a database of document containers. XML documents are stored and indexed in their native format using Berkeley DB as the transactional database engine.

Download Website Updated 02 Dec 2009 Bio2RDF

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Pop 28.35
Vit 2.50

The Bio2RDF software is a package which resolves bio2rdf.org semantic Web identifiers corresponding to bioinformatics data and knowledge bases into RDF files which can be consumed by any generic RDF processor.

No download No website Updated 25 Sep 2012 Bio::SeqReader

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Pop 20.98
Vit 1.00

Bio::SeqReader provides a lightweight alternative to Bioperl when all you really need is a helper for reading sequence data. The Bio::SeqReader::Fastq class correctly handles FASTQ input with multiline sequence or quality data.

No download Website Updated 16 Aug 2005 BioCoRE

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Pop 50.56
Vit 3.03

BioCoRE is a collaborative work environment for biomedical research, research management, and training. It features easy-to-use tools, among them co-authoring papers and other documents, running applications on supercomputers, sharing molecular visualization over the Internet, notifying project team members of recent project changes by email, chatting, keeping a lab book, and other practical features.

No download Website Updated 20 Nov 2002 BioConductor: software for bioinformatics

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Pop 13.93
Vit 1.45

Bioconductor is a set of packages for R (a GPLd statistical data analysis language) which focus on bioinformatics data analysis, especially gene expression arrays (Affymetrix, cDNA spotted arrays). There are tools for statistical normalization, differential expression, genomic visualization, and biological annotation. Future work includes implementation and development of better statistical methods, distributed computing, visualization, and extensions to related high-throughput laboratory assays. The primary developers are research statisticians.

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Open Camera

A camera app for Android.

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mcl-edge

A command-line network analysis workbench.