Search Results for "git:/git.code.sf.net/p/docfetcher/code" - Page 2
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Showing 56 open source projects for "git:/git.code.sf.net/p/docfetcher/code"
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Eurekos LMS - Build a Smarter CustomerEurekos is a purpose-built LMS that engages customers throughout the entire learning journey from pre-sales, to onboarding, and everything after.
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fast_count_multi
Extremely fast NGS read counter
...Files include: fast_count_multi - reports all counts and RPKM, multithreading support fast_count_deseq - reports gene counts in deseq compatible format, multithreading support fast_count - reports all counts with no multithreading support. usage ./fast_count_multi num_threads gtf_file bam_file(s) > output Requires bamtools API library at run time, and c++0x for compile. git clone https://github.com/pezmaster31/bamtools cd bamtools mkdir build cd build cmake .. make export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:path to/lib g++ -I bamtools/include/ -L bamtools/lib/ -o fast_count_multi fast_count_multi.cpp -lz -lbamtools -fpermissive -pthread -std=c++0x -
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DNA patterns & application
A software for generating DNA patterns
... [2] Gagniuc and Ionescu-Tîrgoviste. Gene promoters show chromosome specificity and reveal chromosome territories in humans, BMC Genomics 2013, 14:278. Source code VB6 (Visual Basic 6.0) -
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Reference implementation of the Systems Biology Graphical Notation: map exchange format and library handling import/export and validation. Resource of the libSBGN project have been migrated from SourceForge to GitHub. Latest changes can be found on GitHub now. The code repository can be found here now https://github.com/sbgn/libsbgn The files (releases) can be found here now https://github.com/sbgn/libsbgn/releases The bugs and features (issues) can be found here now https://github.com/sbgn/libsbgn/issues
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Nancy_EX
Quantum Chemistry: Excited States Topology
An open source code for the analysis of electronic excited states: Natural Transition Orbitals; Detachment and Attachment Density Matrices; Quantum Chemical Charge-Transfer Descriptors. The code is intended to postprocess Gaussian 03 and 09 outputs. Important Note: A new release with better compilation option has been released on November the 9th 2015. -
Information Security Made Simple and Affordable | CarbideGet expert guidance and smart tools to launch or level up your security and compliance efforts without the complexity.
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HYBRYD
Library written in C with Python API for IPv6 networking
...I'm trying to readapt it for Python 2.7.3 and GCC 4.6.3 The library has to be build as a simple Python extension using >python setup.py install and allows to create different kind of servers, clients or hybryds (clients-servers) over (TCP/UDP) using the Ipv6 Protocol. The architecture of the code is based on brain architecture. Will put an IPv6 adress active available as soon as possible so that you can download pieces of codes. The aim of that coding was to use primary linux commands easily codable and make an object of an IPv6 connection. Moreover, the model is full-state! -
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PyCancerDB
Cancer Proteomics Database display and management
PyCancerDB is a source code distribution providing a Web-based interface for browsing and updating the Cancer Proteomics Database, together with scripts for maintaining the database. -
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ANT.Gaussian
Quantum transport code based on Gaussian03/09
Atomistic NanoTransport (ANT) comprises a series of codes designed to compute electronic quantum transport with a broad range of applicability in nanoelectronics. ANT.Gaussian (or ANT.G for brevity) relies on the popular quantum chemistry code GAUSSIAN03/09 code with which interfaces in a seamless manner. Straightforwad use of ANT.G include the computation of the zero-bias conductance (or, alternatively, the electrical current under an applied bias voltage) of a variety of nanoscale systems such as molecular bridges or simply metallic atomic contacts as those created with scanning tunneling microscope or break junction techniques. ... -
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RANGE: produce random genetic transcription networks in the NEMO language, which when compiled outputs models in Systems Biology Markup Language. Generate synthetic microarray data, or use NEMO alone to SBML-ize a network, or visualize it in cytoscape.
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[OBSOLETE, check Github repository: https://github.com/LBT-CNRS/MDDriver) MDDriver is a library allowing a user to easily couple molecular visualisation tools with simulation code through a network. It allows to carry out interactive molecular dynamics, visualize simulation results and drive a simulation in interactive time.
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Composable, Open Source Payments PlatformJuspay's Payments Orchestration Platform offers a comprehensive product suite for businesses, including open-source payment orchestration, global payouts, seamless authentication, payment tokenization, fraud & risk management, end-to-end reconciliation, unified payment analytics & more. The company’s offerings also include end-to-end white label payment gateway solutions & real-time payments infrastructure for banks. These solutions help businesses achieve superior conversion rates, reduce fraud, optimize costs, and deliver seamless customer experiences at scale.
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PolySim
Polymer simulation utilites
...It shouldn't be a problem to implement any new specific one (discrete models) 2) off-lattice monte carlo and molecular dynamics (continuous models) Latter one is rebuild of earlier version of simpatico (http://gemini.cems.umn.edu/research/morse/code/simpatico/home.php) project. Input and output are based on PDB file format which is better to visualize with pymol. For specific non-pdb input/output of 2nd program there are convertation utils also available. Programs are expected to compile in gcc under cygwin or pure linux environment. Scripts to run many copies of program under pbs/torque cluster system are also available. -
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NanoCap
Carbon Fullerene and Capped Nanotube Generator
...In addition, the NanoCap core libraries can be used in custom Python scripts that enabled the user to produce structures in bulk or to include the structure generation routines into pre-existing code. -
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IQuant
A pipeline for quantitative proteomics based upon isobaric tags
...This website contains the IQuant software, an example data labeled by iTRAQ-8plex for testing and a user's manual. If you have any question about IQuant, please contact me: wenbo@genomics.cn. The source code of IQuant can be found here "https://sourceforge.net/p/iquant/code/". -
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SPADE
A toolkit for developing and deploying protein structure algorithms.
The Structural Proteomics Application Development Environment is a Python tool kit for developing and deploying bioinformatics applications. Handles graphics, analysis, and modeling of protein sequence and structure. Source and Win installers available. SPADE source code can be cloned from http://www.github.com/deaconjs/SPADE. -
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SIMtoEXP
For comparison of simulation and experimental scattering data
...It also calculates volume probability distributions according to a space filling volumetric model. Written in C++ and Qt, SIMtoEXP has a very simple and easy to use GUI with interactive plotting. The software was originally developed by Norbert Kucerka. The code has been tested on OpenSUSE and Ubuntu (both binary and compilation); Windows and Mac are not officially supported, see the 'Notes' in the tar. PLEASE READ THE WIKI FOR THE MOST UP-TO-DATE INFORMATION - there have been major bug fixes recently. -
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This package contains code for use with Short Read DNA Sequencing technologies, and includes packages for ChIP-Seq, Whole Transcriptome Shotgun Sequencing, Whole Genome Shotgun Sequencing, SNP Detection, Transcript expression and file conversion.
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MoleCalc
A molecular weight calculator written in Visual Basic.
A molecular weight calculator written in Visual Basic. Unfortunately, it is only for 64-bit Windows at this time. The code files (.sln) are downloadable only. I can't figure out Git. -
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nwhess2freq
Calculates frequencies/modes from an nwchem generated hessian
...The advantage of having a separate script for this is that you can use the same hessian to calculate frequencies for different isotopic substitutions i.e. you only have to run one nwchem calculation. The script is finished in its current form in the sense that it is feature complete. Feel free to amend, translate, copy, steal etc. See the README in the code repository for instructions. Installation: Simply download the file and start Octave in the download directory. -
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Starch CLD fit
Least-squares fit of amylopectin chain-length distribution
...The amylopectin CLD biosynthesis model used by this program is explained in the article “A Parameterized Model of Amylopectin Synthesis provides key insights into the Synthesis of Granular Starch”, by Alex Chi Wu, Matthew K. Morell and Robert G. Gilbert. The downloadable .zip file contain the main code readily usable after compiling. An instruction manual is also provided. This is an open source program. -
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Assembly of mixed genomes
Scripts used to assemble and deconvolute mixed mitochondrial genomes.
Perl scripts used in the paper "Index-free de novo assembly and deconvolution of mixed mitochondrial genomes" by McComish BJ, Hills SFK, Biggs P and Penny D (2010) Genome Biology and Evolution 2:410-424. -
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EPLF
Electron Pair Localization Function
The Electron Pair Localization Function (EPLF) helps to understand chemical bonding in molecular systems. This code uses a modified formulation which allows the exact calculation of the EPLF for usual wave functions (HF,KS,CAS,...) -
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Smoldyn is a computer program for simulating reactions and diffusion at a mesoscopic size scale. This scale lies between the more traditional microscopic size scale, in which all or most atoms are considered.
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The Protein Geometry Database hosts the development code for a flexible database for searching protein geometry, as well as a library for accessing this data for protein modeling & refinement programs.
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MOLGENIS can be used to generate databases for life science experiments (micrroarray, mass spectrometry, genomics) having a web user interface, csv exchange format, and programmatic interfaces (web services, rest, and r-project). See NatRevGen 8.
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SynBioLib -- your toolkit for synthetic biology applications. SynBioLib aims to establish a platform on which the Synthetic Biology community can develop and share code that is common to many tasks and programs.
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The Blue Obelisk is a group of scientists driven by a belief in Open Source, Open Standards and Open Data, expressed in code, data, algorithms, specifications, tutorials, demonstrations, articles and anything that helps get the message across.
