Search Results for "informatics" - Page 12
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Showing 2481 open source projects for "informatics"
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N2A
Neurons to Algorithms - A neural modeling and simulation workbench
"Neurons to Algorithms" (N2A) is a language for modeling neural systems, along with a software tool for editing models and simulating them. N2A is currently "alpha" software. The download provided on SF is for convenience to those who wish to preview the software. Please see our site on github for development status. -
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OpenChrom is a tool for gas chromatography and mass spectrometry. The focus is to handle data files from different GC/MS and GC/FID systems and vendors. Its functionality and algorithms can be extended using a flexible plugin approach, based on Eclipse RCP.
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Meraculous-2D
Eukaryotic Genome Assembler
---------------------------------------- IMPORTANT: Meraculous-2D has been superseded by the HipMer assembler, available here: https://sourceforge.net/projects/hipmer/ ----------------------------------------- Meraculous-2D is a whole genome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... -
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SIBsim4: an extensive rewrite of the sim4 program to improve execution speed and provide more informative output. Written in C, mainly targeted at Linux and Unix. Keywords: bioinformatics, genome, transcriptome, EST, splicing, exon, intron.
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OptFlux is an open-source and modular software aimed at being the reference computational application in the field. It is the first tool to incorporate strain optimization tasks, i.e., the identification of Metabolic Engineering targets.
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BioSeq
A simple GUI for some of the biological sequence analysis.
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Tagger is a tool which allows searching fixed-sequence tags (or sequence branches) against entire genomes or mRNA reference sequence databases.
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PPICompare
detection of rewiring events in protein interaction networks
PPICompare detects statistically significant rewiring events in protein-protein interaction networks - even if they are caused by alternative splicing - and reports plenty of information to that. The input data needs to be constructed with PPIXpress (see https://sourceforge.net/projects/ppixpress/). The original publication can be found on https://bmcsystbiol.biomedcentral.com/articles/10.1186/s12918-017-0400-x. -
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MANTIS R Package
Multi-locus ANTIgenic Simulator R-package for multi-strain pathogens
This repository contains the most updated code version of MANTIS, the Multi-locus ANTIgenic Simulator R-package. MANTIS is developed and maintained by the Evolutionary Ecology of Infectious Disease (EEID) research group at the Department of Zoology, University of Oxford, UK. For theoretical background please refer to 'MANTIS: an R package that simulates multilocus models of pathogen evolution' (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0598-9 OPEN... -
MongoDB Atlas runs apps anywhereMongoDB Atlas gives you the freedom to build and run modern applications anywhere—across AWS, Azure, and Google Cloud. With global availability in over 115 regions, Atlas lets you deploy close to your users, meet compliance needs, and scale with confidence across any geography.
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...Java code developed by the Australian ICGC team for operating on next-generation sequencing data. This code is currently being maintained and expanded by the QIMR Berghofer Genome Informatics team (http://www.qimrberghofer.edu.au/lab/genome-informatics/) More details and documentation can be found on the wiki: http://sourceforge.net/p/adamajava/wiki/Home/
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The Disease Ontology has moved to Github. New project page: https://github.com/DiseaseOntology Disease Ontology is a stuctured controlled vocabulary originally based upon and mapped to medical billing codes. The goal of this ontology is to create a comprehensive hierachical controlled vocabulary to represent subsumptive disease relationships.
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JSiteDescriptor
Binding site descriptor generation for SVM based classification.
A set of java programs that extract coordinate and chemical information from PDB files. The binding site regions are extracted using grid based scheme. For binding site, spatio-chemical descriptor is generated based on PocketMatch algorithm of Dr. Kalidas (author of this project too). -
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GPU MrBayes implements MrBayes MC(3) on the GPU using CUDA. When using our program in your article, please cite our paper "Efficient Implementation of MrBayes on multi-GPU" (http://mbe.oxfordjournals.org/content/early/2013/03/14/molbev.mst043.abstract.html?papetoc).
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D-Tailor
D-Tailor: automated analysis and design of DNA sequences
Recent advances in DNA cloning and synthesis technologies afford high throughput implementation of designed sequences into living cells. However, our ability to design sequences to interrogate multifactorial biological processes and further engineer biological functions is lagging behind. DNA-Tailor (D-Tailor) is a fully extendable software framework for biological sequence analysis and multi-objective sequence design. D-Tailor permits the seamless integration of an arbitrary number of... -
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Pipebar
A fast and accurate pipeline for DNA barcoding analysis.
Molecular analyses require the use of multiple bioinformatics tools. Here we proposed a pipeline for DNA chromatograms analysis of Sanger platform by open-source tools integration in order to reduce cost with standard commercial licences ensuring high quality, robustness with reduced time. Pipebar is a python application created to automatization of processing chromatogram trace files to high-quality DNA sequences for downstream analyses. -
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CSBB-v2.1 [CSBB-v3.0 is now available]
Computational Suite For Bioinformaticians and Biologists
CSBB is a command line based bioinformatics suite to analyze biological data acquired through varied avenues of biological experiments. CSBB is implemented in Perl, while it also leverages the use of R, java and ruby in background for specific modules. Major focus of CSBB is to allow users from biology and bioinformatics community, to get benefited by performing down-stream analysis tasks while eliminating the need to write programming code. CSBB is currently available on Linux, UNIX and... -
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BWTT
BIOTACT Whisker Tracking Tool
The BWTT is an artefact of the EU Framework 7 Project BIOTACT 215910. It is an extensible software framework that runs under Matlab (Mathworks, TM) providing for the computation of whisker tracking algorithms for small mammal observation. Other tracking algorithms (e.g. snout tracking) can also be included. The software is released with a number of algorithms included, allowing rapid whisker tracking with no other software required (other than Matlab). -
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Genobuntu
Genobuntu Package for Next Generation Sequencing
Genobuntu is a software package containing more than 70 software and packages oriented towards NGS. In its current version, Genobuntu supports pre assembly tools, genome assemblers as well as post assembly tools. Commonly used biological software and example script files for different assembly pipelines have also been provided, where the example script files can be updated to suit one’s experimental needs. Genobuntu attempts to reduce the amount of time and energy needed to build ... -
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CSBB-v3.0
CSBB - Computational Suite for Bioinformaticians and Biologists
CSBB is a command line-based bioinformatics suite to analyze biological data acquired through varied avenues of biological experiments. CSBB is implemented in Perl, while it also leverages the use of R, java, python and ruby in background for specific modules. Major focus of CSBB is to allow users from biology and bioinformatics community, to get benefited by performing down-stream analysis tasks while eliminating the need to write programming code. CSBB is currently available on Linux,... -
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Taxoblast
Taxoblast is a pipeline to identify contamination in genomic sequence
Raw genomic sequences are frequently contaminated with sequences of other organism. Their identification is essential for the interpretation of genomic data. In this context it is essential to distinguish between horizontal gene transfers and contamination. The genomic context of sequences can help distinguish the two scenarios. Taxoblast splits genomic scaffolds into sub-sequences of defined length and for each of them determines the closest related taxon. It then summarizes this... -
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ProteoWizard development moved to GitHub in 2018. The ProteoWizard Library is a set of software libraries and tools for rapid development of proteomics data analysis software. The libraries are cross-platform and built from the ground up using modern C++ techniques.
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Electronic Health Records system inspired by research at the Centre for Health Informatics, City University, London, and developed using the principles of Open Health Informatics. This project is no longer updated on sourceforge. The latest release of cityEHR can now be downloaded at openhealthinformatics.org
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LBXR - LOAD BLAST XML RESULTS O sistema permite que sejam importados resultados obtidos por meio de pesquisas de similaridade a partir do BLAST, com resultados gerado no formato XML para o banco de dados relacional MariaDB ou MySQL.
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HIGH-THROUGHPUT TABULAR DATA PROCESSOR (HTDP) is Java application that is intended to facilitate data exploration and reduction tasks in large text files resulting from high throughput technologies, e.g. massively parallel sequencing or microarrays. The software has been optimized for microarray and deep parallel sequencing data, however it can accept any character delimited tabular data sets. HTDP can also import, process and convert Variant Call Format (VCF) files ver. 4.0, 4.1 and 4.2...