Open Source Linux Bio-Informatics Software

Bowtie, an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers. Please cite: Langmead B, et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25.

OpenClinic GA is an open source integrated hospital information management system covering management of administrative, financial, clinical, lab, x-ray, pharmacy, meals distribution and other data. Extensive statistical and reporting capabilities.

Open Information Systems for Emergency Services (Open ISES) is a community of software developers, paramedics, EMTs, law enforcement & fire fighters working together to create open source software & training materials for the emergency service community.

The Systems Biology Workbench(SBW) is a framework for application intercommunications. It uses a broker-based, distributed, message-passing architecture, supports many languages including Java, C++, Perl & Python, and runs under Linux,OSX & Win32. It comes with a large number of modules, encompassing the whole modeling cycle: creating computational models, simulating and analyzing them, visualizing the information, in order to improve the models. All using community standards, such as SED-ML, SBML and MIRIAM.

3D viewer which arranges BLAST hits and other bioinformatics-related alignments in a rotating, cylindrical display. Feedback appreciated. NOTE: requires Java3d installation. Superceded by Cylindrical Alignment App

A base for programs. Includes algorythms for Q-learning and SOM's etc. too. Examples: Hamron: Simulates evolution, uses the 2D-renderer. DriveUnit: created for school, for a robotic arm, uses the 3D-renderer. Hlearn: http://www.sagenb.org/home/pub/8

Free operating system for biorobots. If you biorobot, you can download an installation image of our OS is directly from here...

Bio-SPHERE aims to create a flexible, secure and multimodal biometric platform for applications that require biometrics. Bio-SPHERE is formed by a network of interacting nodes that interface with biometric hardware and offer biometric functions.

It moves by itself inside networks like virus infection & plagues, it is being written to solve computer virus problem drastically and responsibly. It is legal, free and open for public domain to improve W3 ICT Security.

Source code for the Chemical Informatics and Cyberinfrastructure Collaboratory project.

Cervelletto is a neural network simulator. It uses a new neural model based on biological, neurological and psychological studies. [it's not yet completed... just give me some weeks! sorry!]

Cluster Networks are a new style of neural simulation / neural network modeling, that models networks of neural populations ("clusters") that transform and transmit information using precisely-timed, graded bursts ("pulses" or "volleys") of firing.

Virtual machine/emulator; "holding pen" for self-replicating programs written in custom RISC assembly-like language, evolving via random point mutations and periodic fitness-based cullings. Inspired (like Avida) by Thomas Ray's alife simulator, Tierra

One goal of sequencing based metagenomic analysis is the quantitative taxonomic assessment of microbial community compositions. However, the majority of approaches either quantify at low resolution (e.g. at phylum level) or have severe problems discerning highly similar species. Yet, accurate quantification on species level is desirable in applications such as metagenomic diagnostics or community comparison. GASiC is a method to correct read alignment results for the ambiguities imposed by similarities of genomes. It has superior performance over existing methods. You can find the accompanying paper here: http://nar.oxfordjournals.org/content/41/1/e10.short Thanks to the great work of the SeqAn team, you can now use GASiC as a Knime workflow: https://github.com/seqan/knime_seqan_workflows/tree/master/metagenomics_gasic_workflow

OpenEMS™ is the multi platform Grid framework to seamlessly aggregate all your multi platform resources into a virtual super computer.

GridSweeper makes it easy to perform batch runs of scientific simulation programs on computational grids/distributed resource management systems.

Gridder is a group of portlets that simplify the use and administration of grid services. Especially for job submission management. Gridder also extends and documents the functionality of the OGCE Bundle. It is plenty of useful documentation.

Open Source project for the development of the IEEE 11073-20601 reference implementation.

Info Sapient will be an Open Source, Common License 0.5, 100% Pure Java based program that is a mechanism for the expression and execution of business rules.

Platform for parallel computation in the Amazon cloud, including machine learning ensembles written in R for computational biology and other areas of scientific research. Home to MR-Tandem, a hadoop-enabled fork of X!Tandem peptide search engine.

IslandEv distributes a Genetic Algorithm (like <a href="/projects/jaga">JaGa</a>) across a network (see <a href="/projects/distrit">DistrIT</a>) using an island based coevolutionary model in which neighbouring islands swap migrating individuals every

The primary goal of the JES is to develop Distributed Configuration Service for client/server,clusters,grids,agent based architectures.

The Java Batch System (JBS) is a batch queueing system in the tradition of NQS and PBS for internal (Java-based) and system batch jobs. Stand-alone operation and integration with existing batch queueing systems, initially OpenPBS, is supported.

Jaybird is java-language based, source & xml & codebyte class inter-converting tool. You can write your Envolvable Code with it; You can make your computer write program itself; You can run program without compiling time; You can manage source as data

---------------------------------------- IMPORTANT: Meraculous-2D has been superseded by the HipMer assembler, available here: https://sourceforge.net/projects/hipmer/ ----------------------------------------- Meraculous-2D is a whole genome assembler for NGS reads (Illumina) that is capable of assembling large, diploid genomes with modest computational requirements. Features include: - Efficient k-mer counting and deBruijn graph traversal - Two modes of handling of diploid allelic variation - Improved scaffolding that produces more complete assemblies without compromising scaffolding accuracy. The assembly is driven by a perl pipeline which performs data fragmentation and load balancing, as well as submission and monitoring of multiple task arrays on a GE/SLURM-type cluster or a standalone multi-core server. Manuscripts in submission: https://arxiv.org/abs/1703.09852 https://arxiv.org/abs/1608