Search Results for "https c lib"
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Showing 26 open source projects for "https c lib"
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Build Agents and Models on One PlatformGemini Enterprise Agent Platform is Google Cloud's comprehensive platform for developers to build, scale, govern, and optimize agents and models. Choose from Google's most advanced models and third-party models like Anthropic's Claude Model Family.
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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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CpDB
Relational database schema and tools for bacterial genome annotation
This software allows us to create a relational database in PostgreSQL hosting full bacterial genomes. Besides the database, there is software, like a parser, to convert EMBL or GBK files to the CpDB relational schema. Once in the CpDB, one can extract unlimited reports from bacterial genomes using SQL. This software is part of the Ph.D. in Bioinformatics from Anderson Santos (https://orcid.org/0000-0003-3418-0823) developed under the Corynebacterium pseudotuberculosis (Cp) pangenome project.... -
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DEEP
Differential Evolution Entirely Parallel Method
The Differential Evolution, introduced in 1995 by Storn and Price, considers the population, that is divided into branches, one per computational node. The Differential Evolution Entirely Parallel method takes into account the individual age, that is defined as the number of iterations the individual survived without changes. The introduced improvements are: (I) allow several oldest individuals to be overwritten by the same number of best ones in the population, (II) new selection rule uses... -
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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 -
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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uac19
Analyze COVID-19 csv files
A flexible command line tool to analyze COVID-19 csv files https://github.com/nytimes/covid-19-data https://ourworldindata.org/coronavirus-source-data The rpm build is rh7 the tgz installs on Windows cygwin. -
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Comet MS/MS search engine
Comet open source tandem mass spectrometry (MS/MS) search engine.
September 2021: the code repository has migrate to https://github.com/UWPR/Comet Comet is an open source tandem mass spectrometry (MS/MS) sequence database search engine. It identifies peptides by searching MS/MS spectra against sequences present in protein sequence databases. Comet currently exists as a simple Windows or Linux command line binary that only does MS/MS database search. Supported input formats are mzXML, mzML, ms2, and Thermo RAW files. Supported output formats are... -
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MAGeCK
Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout
MAGeCK2 is here: https://github.com/davidliwei/mageck2 Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. For instructions and documentations, please refer to the wiki page. MAGeCK is developed by Wei Li and Han Xu from Dr. Xiaole Shirley Liu's lab at Dana-Farber Cancer Institute/Harvard School of Public Health, and is maintained by Wei Li lab at... -
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MrBayes is a program for the Bayesian estimation of phylogeny. The project has been moved to GitHub: https://github.com/NBISweden/MrBayes
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lr2rmats
Long read to rMATS
lr2rmats is a Snakemake-based light-weight pipeline which is designed to utilize both third-generation long-read and second-generation short-read RNA-seq data to generate an enhanced gene annotation file. The newly generated annotation file could be provided to rMATS for differential alternative splicing analysis. More information can be found at https://sourceforge.net/p/lr2rmats/wiki/Home/ -
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NOTE: Use of this codebase is NOT RECOMMENDED. This project has been migrated to github at http://jaerproject.net (or https://github.com/SensorsINI/jaer for the Java code). Commits have been disabled for the subversion sourceforge repository and new development is being done on the github repository. Java tools for Address-Event Representation (AER) neuromorphic processing. Uses USB hardware. See wiki at https://sourceforge.net/p/jaer/wiki/
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Stochastic simulator for signaling pathways occuring in biological cells. Handles reaction-diffusion processes in 3D tetrahedral meshes. Please check our new repository: https://github.com/CNS-OIST/STEPS
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**** This page is not used for this project any longer. *** Please update your bookmarks and go to https://github.com/UUPharmacometrics/PsN
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LDhat
Estimate Recombination Rates from Population Genetic Data
LDhat is a package written in the C language for the analysis of recombination rates from population genetic data. This package has migrated to github: https://github.com/auton1/LDhat -
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TransGeneScan
TransGeneScan is a gene finding tool for metatranscriptomic sequences
NOTE: TransGeneScan is migrated to Github (https://github.com/COL-IU/TransGeneScan). TransGeneScan is no longer maintained in SourceForge. Please find the latest version in Github. TransGeneScan is a gene finding tool for Metatranscriptomic sequences. TransGeneScan incorporates strand-speci c hidden states, representing coding sequences in sense and anti-sense strands on transcripts in a Hidden Markov Model similar to the one used in FragGeneScan (http://fraggenescan.sourceforge.net/), and can predict a sense transcript containing one or multiple genes (in an operon) or an antisense transcript. -
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SOAPdenovo-Trans
A de novo transcriptome assembler.
Latest Codes on GitHub: https://github.com/aquaskyline/SOAPdenovo-Trans SOAPdenovo-Trans is a de novo transcriptome assembler inherited from the SOAPdenovo2 framework, designed for assembling transcriptome with alternative splicing and different expression level. The assembler provides a more comprehensive way to construct the full-length transcript sets compare to SOAPdenovo2. -
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SOAP3-DP
Fast, Accurate and Sensitive GPU-based Short Read Aligner
...SOAP3-dp natively supports BAM file format and provides the same scoring scheme as BWA, which enables it to be integrated into existing analysis pipelines. Citation: Luo R, Wong T, Zhu J, Liu C-M, Zhu X, et al. (2013) SOAP3-dp: Fast, Accurate and Sensitive GPU-Based Short Read Aligner. PLoS ONE 8(5): e65632. doi:10.1371/journal.pone.0065632 -
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dna-bison
Bisulfite alignment On Nodes of a cluster
Bison allows users with access to a computer cluster to rapidly align whole-genome bisulfite sequencing or RRBS reads. It can align both directional and non-directional libraries and uses bowtie2. Multiple compute nodes are not absolutely required, but will make the alignment process faster. Further details available on the Wiki page. Help also available on SEQanswers (http://seqanswers.com/forums/showthread.php?t=31314) or by creating a ticket here. You can now track the... -
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This space is not maintained anymore. If you want to get the latest updates on fpocket refer to https://github.com/Discngine/fpocket. Fpocket is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. The platform is suited for the scientific community willing to develop new scoring functions and extract pocket descriptors on a large scale level.
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NeedlemanWunsch
Fast global sequence alignment for the masses!
MOVED TO GITHUB: https://github.com/noporpoise/seq-align Global optimal sequence alignment using the Needleman-Wunsch algorithm. Aligns DNA, RNA, protein sequence and more! See our sister project local alignment using Smith-Waterman: http://sourceforge.net/projects/smithwaterman/ -
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The project has moved to GitHub: https://github.com/pixmeo/osirix
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SmithWaterman
Fast local sequence alignment for the masses!
MOVED TO GITHUB: https://github.com/noporpoise/seq-align An implementation of the Smith-Waterman local sequence alignment algorithm. See our sister project global alignment using Needleman-Wunsch: http://sourceforge.net/projects/needlemanwunsch/ -
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MASyV (Multi-Agent System Visualization) enables one to write agent-based models/cellular automata, eg. in C, visualize them in real time & capture to movie file with MASyVs GUI & message passing lib. Includes examples: Hello World, ants, viral infection
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The SBML ODE Solver is a command-line tool and programming library (ISO/ANSI C) for construction and numerical integration of an ODE system, derived from an SBML based description of a biochemical reaction network. Development has moved to https://github.com/raim/SBML_odeSolver . Please download the latest version from there!
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RADAR stands for Rapid Automatic Detection and Alignment of Repeats in protein sequences. RADAR identifies gapped approximate repeats and complex repeat architectures involving many different types of repeats. Radar has moved to github (https://github.com/AndreasHeger/radar)
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>>> MIA has been moved to GitHub! <<< Please use the new Location: https://github.com/udo-stenzel/mapping-iterative-assembler =========================================================
