Search Results for "gnu on windows"
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Showing 996 open source projects for "gnu on windows"
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Bowtie 2
A fast and sensitive gapped read aligner
Bowtie 2 is a fast, memory-efficient genomic read aligner used to map sequencing reads against long reference sequences such as mammalian genomes. It is especially effective for reads ranging from around 50 bases to hundreds or thousands of characters, and it supports modern sequencing workflows that require gapped, local, and paired-end alignment. The tool builds compact FM-index-based reference indexes, keeping memory usage low even for large genomes like the human genome. Bowtie 2 outputs... -
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Free DELTA
Software tools for processing taxonomic descriptions in DELTA format
The Free DELTA Project is a free, open-source, software alternative for a generic system to the processing of taxonomic descriptions based on the DELTA (DEscription Language for TAxonomy) format. -
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Jmol
An interactive viewer for three-dimensional chemical structures.
Over 1,000,000 page views per month. Jmol/JSmol is a molecular viewer for 3D chemical structures that runs in four independent modes: an HTML5-only web application utilizing jQuery, a Java applet, a stand-alone Java program (Jmol.jar), and a "headless" server-side component (JmolData.jar). Jmol can read many file types, including PDB, CIF, SDF, MOL, PyMOL PSE files, and Spartan files, as well as output from Gaussian, GAMESS, MOPAC, VASP, CRYSTAL, CASTEP, QuantumEspresso, VMD, and many other... -
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The Sashimi project hosts the Trans-Proteomic Pipeline (TPP), a mature suite of tools for mass-spec (MS, MS/MS) based proteomics: statistical validation, quantitation, visualization, and converters from raw MS data to the open mzML/mzXML formats.
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The Chemistry Development Kit (CDK) is a scientific, LGPL-ed library for bio- and cheminformatics and computational chemistry written in Java. The main home page of the CDK is now at: http://cdk.github.io
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BioXTAS RAW
Processing and analysis of Small Angle X-ray Scattering (SAXS) data.
BioXTAS RAW is a program for analysis of Small-Angle X-ray Scattering (SAXS) data. The software enables: creation of 1D scattering profiles from 2D detector images, standard data operations such as averaging and subtraction, analysis of radius of gyration (Rg) and molecular weight, and advanced analysis using GNOM and DAMMIF as well as electron density reconstructions using DENSS. It also allows easy processing of inline SEC-SAXS data and data deconvolution using the evolving factor analysis... -
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Conscious Artificial Intelligence
It's possible for machines to become self-aware.
This project is a quest for conscious artificial intelligence. A number of prototypes will be developed as the project progresses. This project has 2 subprojects: Object Pascal based CAI NEURAL API - https://github.com/joaopauloschuler/neural-api Python based K-CAI NEURAL API - https://github.com/joaopauloschuler/k-neural-api A video from the first prototype has been made: http://www.youtube.com/watch?v=qH-IQgYy9zg Above video shows a popperian agent collecting mining ore from 3... -
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AMBIT:Chemical Structure DB&Web Service
Chemical structures database & machine learning with web services API
AMBIT offers a cheminformatics data management for chemical substances, structures and nanomaterials. Flexible structure, similarity and study queries storage, descriptor calculation and predictive models building via REST web services.User interface for creating read across assessment and generating reports, aligned with regulatory and industrial requirements. Command line applications also available. Integration with third party tools and databases. -
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relax
Molecular dynamics by NMR data analysis
The software package 'relax' is designed for the study of molecular dynamics through the analysis of experimental NMR data. Organic molecules, proteins, RNA, DNA, sugars, and other biomolecules are all supported. It supports exponential curve fitting for the calculation of the R1 and R2 relaxation rates, calculation of the NOE, reduced spectral density mapping, the Lipari and Szabo model-free analysis, study of domain motions via the N-state model and frame order dynamics theories using... -
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A software package that implements the probabilistic record linkage technique (PRL). This is a new, improved, open-source, multi-platform version of the previously available program, by the same authors.
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NGSEP
NGSEP (Next Generation Sequencing Experience Platform)
NGSEP is an integrated framework for analysis of short and long DNA high throughput sequencing reads. The current version provides functionalities for both de-novo and reference guided analysis of sequencing data, including genome assembly, read mapping, variants detection and genotyping and de-novo analysis of data generated from reduced representation protocols. NGSEP also provides modules for analysis of genomic variation databases (VCF files), including functional annotation, filtering,... -
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janda
structural variant detector
Janda is a tool to detect structural variants in whole-genome DNA sequence data. It identifies structural variants (deletions, duplications, translocations, and inversions) using anomalously mapped pair reads and realigning potential junction reads. -
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The MolTools Java library provides tools for building applications that handle nucleotide sequence data. Features include sequence I/O, handling of lists/databases of sequences, calculation of Tm, and other utilities for sequence design.
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PFAAT is a Java-based multiple sequence alignment editor and viewer designed for protein family analysis. You can download PFAAT from http://pfaat.sourceforge.net/
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ProStack
ProStack - a platform for image processing and analysis
ProStack - a platform for image processing and analysis. It implements various image processing methods as separate modules, that can be joined in a complex image processing scenario by use of a graphical user interface. RPMs are available at https://build.opensuse.org/project/repositories/home:mackoel:compbio -
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In addition to computing co-expression clusters, Maccu fishes potential co-expressed genes for a given bait set. All results can be further processed via graph-level operations so that we can compare graphs based on different reference data.
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GOBU
Gene Browsing Utility
Gene Ontology Browsing Utility (hereinafter, GOBU, pronounced as "go-boo") is a browsing and manipulating tool for Post-Pipeline genetic data, especially useful for data with GO annotations. With help of GOBU, we expect biologists and their cooperating technicians can pay less effort on common programming stuff. At the same time, GOBU provides an Extendable Architecture which guarantees the possibility of 1. Arbitrary Data Description, 2. Data Integration, and 3. Extendable User Interface. -
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In addition to RPKM (Reads Per Kbp per Million reads) values, RACKJ computes read counts for exons and splicing events. In so doing, it is feasible to compare two samples and identify genes with most significant difference in exon(splicing)-level.
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miRDeep*
MiRDeep*
Please cite: An, J., Lai, J., Lehman, M.L. and Nelson, C.C. (2013) miRDeep*: an integrated application tool for miRNA identification from RNA sequencing data. Nucleic Acids Res, 41, 727-737. We will create index for you if you tell us your interested species (j.an@qut.edu.au). download command line version "MDS_command_line_Vxx.zip" clicking "Browse All Files" please find miRPlant in sourceforge for plant miRNA prediction. -
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Croizat
A software package for quantitative analysis in Panbiogeography
Croizat is a free, user-friendly, cross-platform desktop software package which biologists can use to integrate and analyze spatial data on species or other taxa and to explore geographical patterns in diversity under a panbiogeographic and graph-theoretic approach. -
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NeuroML is an XML-based description language for defining and exchanging neuronal cell, network and modeling data including reconstructions of cell anatomy, membrane physiology, electrophysiological data, network connectivity, and model specification
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CIERA
Crop Information Engine and Research Assistant
CIERA is a data management system for multi-crop breeding programs. It handles the genealogy, phenotypic and genotypic data of most modern breeding programs. It is distributed under the GNU General Public License, Version 3. ** This site is under construction, as of June 2024. *** -
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ProbeMaker is a framework for design of sets of oligonucleotide probes. It allows the design of different types of probes made up of separate sequence elements. A Plug-in mechanism allows extension of the framework with new functionalities.
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mzMatch is a Java collection of small commandline tools specific for metabolomics MS data analysis. The tools are built on top of the PeakML core library, providing mass spectrometry specific functionality and access to the PeakML file format.
