A file format for exchanging computational models in systems biology
The Systems Biology Markup Language (SBML) is an XML-based description language for representing computational models in systems biology. Visit the project web site to learn more.
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/
A web-based interface for system administration of UNIX
A web-based system administration tool for Unix servers and services.
Database connection pool with support for lots of languages and databases.
The Elvira project is a suite of tools to perform high-throughput genomic assemblies of repetitive, structured samples such as viruses or targeted regions of larger genomes.
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.
Uniform interface to computing and data resources
UNICORE is a software suite for building federated systems, providing secure and seamless access to heterogeneous resource such as compute clusters and file systems. More: www.unicore.eu
quattor is a system administration toolkit providing a powerful, portable and modular toolsuite for the automated installation, configuration and management of clusters and farms running UNIX derivates like Linux and Solaris. Quattor no longer uses SourceForge for hosting, please see http://github.com/quattor for source code and http://www.quattor.org for more up-to-date information about the project.
Open Source Software
Open Source Software by Adrian Immanuel Kieß.
eGuideDog project develops free software for the blind. Currently, we focus on WebSpeech, Ekho TTS and WebAnywhere.
This is software to create web dictionaries, esp. for Esperanto like Reta Vortaro (http://reta-vortaro.de). A dictionary is made from articles written in a special XML dialect by transformations using XSLT, ant and some Java code.
Mobile P2P App - Use a P2P App on your Smartphone
This Project shows how to create a mobile smartphone app with a gnutella p2p application. It consits of smartphone java sourcecode, documentation, phex source code, phex proxy and instructions to create a working app. https://www.artikelschreiber.com/en/ This project once was coded with only 2000€ buget and has given revenue of over 30.000€. Happy hacking the java,perl,php code.
Crossfire is graphical multi-user 2d tile-based role playing game.
Crossfire is graphical multi-user 2d tile-based role playing game similar to Moria, Angband, Omega, Nethack, Rogue, Gauntlet, and Muds. The bulk of the game is based on predefined maps, however some areas are randomly generated.
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.
Autopsy® is a digital forensics platform and graphical interface to The Sleuth Kit® and other digital forensics tools. It can be used by law enforcement, military, and corporate examiners to investigate what happened on a computer. You can even use it to recover photos from your camera's memory card.
The home page of the Goddard Mission Services Evolution Center (GMSEC) Application Programming Interface (API).
OMLX project is a place for processing of many projects to be ready to become open source projects.
This is a C library to check the validity of German and Austrian Bank Account Numbers. All currently defined test methods by Deutsche Bundesbank (Dec 2017: 00 to E4) are implemented. Modules for AWK, Perl, PHP, Python, Ruby, C#.net and VB.net are included too. The package includes also an IBAN converter to generate (german) IBANs and BICs from account data. All currently defined IBAN rules by Deutsche Bundesbank are implemented (Dec 2017: 57 rules) and tested against independent solutions.
Software Unit Tests (Language Independent Approach)
Automation of Unit and System Tests. Tests can be implemented in any language and on many platforms. The flexible approach enables the inclusion of many types of tests, such as memory leak checks (using valgrind), coding rule checks, complexity checks, etc. Tests are run by a simple call to hwut in a base directory of a project. In particular for C, HWUT supports make file generation using 'sos' and 'sols' modes. Remote control-able function stubs may be generated using the 'stub' mode. Test cases can be generated using the 'gen' mode, and state machine walkers by the 'sm_walker' mode. Over the last decade HWUT has matured towards a full fledged unit test tool for a wide variety of applications.
Bisulfite-seq/NOMe-seq SNPs & cytosine methylation caller
Now in Github: https://github.com/dnaase/Bis-tools/tree/master/Bis-SNP BisSNP is a package based on the Genome Analysis Toolkit (GATK) map-reduce framework for genotyping in bisulfite treated massively parallel sequencing (Bisulfite-seq, NOMe-seq and RRBS) on Illumina platform. It uses bayesian inference with either manually specified or automatically estimated methylation probabilities of different cytosine context(not only CpG, CHH, CHG in Bisulfite-seq, but also GCH et.al. in other bisulfite treated sequencing) to determine genotypes and methylation levels simultaneously. It works for both of single-end and paired-end reads.Specificity and sensitivity has been validate by Illumina IM SNP array. In default threshold 30X data (Phred scale score > 20), it could detect 92.21% heterozygous SNPs with 0.14% false positive rate Cytosine calling is not only based on reference context, so it could detect non-reference cytosine context. Google group for help: http://goo.gl/zL7Nj
Crystal Space is an Open Source 3D SDK for Unix, Windows, and MacOS/X. It renders with OpenGL and features GLSL shaders, CG shaders, deferred rendering, dynamic shadows, bullet based physics library, terrain engine, skeleton based animation meshes, exporter for Blender, portals, etc...
City of Hope CpG Island Analysis Pipeline
COHCAP (City of Hope CpG Island Analysis Pipeline) is an algorithm to analyze single-nucleotide resolution methylation data (Illumina 450k methylation array, targeted BS-Seq, etc.). It provides QC metrics, differential methylation for CpG Sites, differential methylation for CpG Islands, integration with gene expression data, and visualization of methylation values. Please note: 1) The standalone version of COHCAP is no longer being updated. Please see the Bioconductor version: http://bioconductor.org/packages/release/bioc/html/COHCAP.html 2) In addition to the original NAR paper, please see the following links: Benchmarks: http://www.nature.com/protocolexchange/protocols/2965#/introduction Protocol Exchange Files: http://sourceforge.net/projects/cohcap/files/Protocol_Exchange_Example.zip 3) Bioconductor Custom Annotation Files (including EPIC Array): https://sourceforge.net/projects/cohcap/files/additional_Bioconductor_annotations.zip/download
Android adb backup extractor and creator
Collection of several utilities to work with android backups
Project name: android-backup-toolkit URL: https://sourceforge.net/p/android-backup-toolkit/ License: various (see individual projects) Authors: various (see individual projects) This project is simply a compilation of the six following projects, both latest source code and binaries: * android-backup-extractor: https://sourceforge.net/projects/adbextractor/ * android-backup-splitter: https://sourceforge.net/p/adb-split/ * android-timestamp-keeper: https://sourceforge.net/projects/androidtimestampkeeper/ * helium-backup-extractor: https://sourceforge.net/p/heliumbackupextractor/ * no-adb-backup-app-lister: https://sourceforge.net/projects/no-adb-backup-app-lister/ * tar-binary-splitter: https://sourceforge.net/projects/tar-binary-splitter/ All the android utilities are bundled in a single package.
Open-source automated grading of programming assignments
Web-CAT is a plug-in based web application for automatically grading programming assignments in many programming languages. This project also provides Eclipse plugins for electronic submission and feedback services directly from the Eclipse IDE. We now use github for source code control (https://github.com/web-cat), although all file releases are still provided here through SourceForge. The CVS repository here is for archival purposes only.