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OpenClinic GA
Open Source Integrated Hospital Information Management System
OpenClinic GA is an open source integrated hospital information management system covering management of administrative, financial, clinical, lab, x-ray, pharmacy, meals distribution and other data. Extensive statistical and reporting capabilities. -
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SPiCEv2.1
Splicing Prediction in Consensus Element
SPiCE is no longer maintained. To access the tool's predictions, please use SPiP, accessible at : https://sourceforge.net/projects/splicing-prediction-pipeline/ or https://github.com/raphaelleman/SPiP If you have questions, please contact me to: r.leman@baclesse.unicancer.fr or raphael.leman@orange.fr v2.1.5 (05/2019) + corr (01/2020): Fix bug for linux version v2.1.4 (03/2019): Proxy management (only for Windows version) v2.1.3 (07/2018): correction bug for first 3' ss import vcf file v2.1.2 (06/2018): Import duplication Simplify import of deletion with one nucleotide Use tryCatch Improving web api connection check -
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BioXTAS RAW
Processing and analysis of Small Angle X-ray Scattering (SAXS) data.
...It also allows easy processing of inline SEC-SAXS data and data deconvolution using the evolving factor analysis (EFA) or the regularized alternating least squares (REGALS) methods. Active source code is now maintained on github: https://github.com/jbhopkins/bioxtasraw To install: Check the instructions available at: http://bioxtas-raw.readthedocs.io/en/latest/install.html and in the Files tab. User guides: RAW guides are available at: http://bioxtas-raw.readthedocs.io/ and in the Files tab. To contact us, see: https://bioxtas-raw.readthedocs.io/en/latest/help.html -
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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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Connect every part of your business to one bank accountNorth One is proudly built for small businesses, startups and freelancers across America. Make payments easily, keep tabs on your money and put your finances on autopilot through smart integrations with the tools you’re already using. North One was built to make managing money easy so you can focus on running your business. No more branches. No more lines. No more paperwork. Get complete access to your North One Account from your phone or computer, wherever your business takes you. Create Envelopes for taxes, payroll, rent, and anything else automatically.
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Hydrogen Bond Analysis Tool (HBAT)
HBAT 2 is migrated from PERL to Python.
HBAT(Hydrogen Bond Analysis Tool) is a tool to automate the analysis of hydrogen bonds present in a PDB Structure file. HBAT 2 is migrated from PERL to Python. Latest Documentation: https://hbat.abhishek-tiwari.com/ Web Server Version: http://hbat-web.abhishek-tiwari.com Latest Github Release: http://github.com/abhishektiwari/hbat Citation: Tiwari, A., & Panigrahi, S. K. (2007). HBAT: A Complete Package for Analysing Strong and Weak Hydrogen Bonds in Macromolecular Crystal Structures. In Silico Biology, 7(6). https://doi.org/10.3233/ISI-2007-00337 -
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QUAST
Quality Assessment Tool for Genome Assemblies
QUAST performs fast and convenient quality evaluation and comparison of genome assemblies. It is maintained by the Gurevich lab at HIPS (https://helmholtz-hips.de/en/hmsb). For the most up-to-date description, please visit http://quast.sf.net. Below are just some highlights. QUAST computes several well-known metrics, including contig accuracy, the number of genes discovered, N50, and others, as well as introducing new ones, like NA50 (see details in the paper and manual). ... -
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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 mining sites and bringing to the base. At the time the agent is born, it doesn't know how to walk nor it knows that it feels pleasure by mining. ... -
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BIGSdb
Software for storing and analysing bacterial sequence data
...These loci can be further organised into schemes for isolate characterisation or for evolutionary or functional analyses. See Jolley and Maiden 2010, BMC Bioinformatics 11:595 (http://www.biomedcentral.com/1471-2105/11/595). You can report bugs or make enhancement requests using the issues tracker at https://github.com/kjolley/BIGSdb. The source code is also mirrored there. -
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Comet MS/MS search engine
Comet open source tandem mass spectrometry (MS/MS) search engine.
...Supported input formats are mzXML, mzML, ms2, and Thermo RAW files. Supported output formats are tab-delimited text, Percolator pin, SQT, and pepXML Documentation and project website: http://comet-ms.sourceforge.net -
Grafana: The open and composable observability platformGrafana is the open source analytics & monitoring solution for every database.
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GelJ
GelJ is a Java program for the analysis of DNA gel fingerprints images
...Some of the outstanding features of GelJ are functionality for accurate lane- and band-detection, several methods for computing migration models and generating dendrograms, comparison of banding patterns from different experiments, and database support. Citing GelJ: J. Heras, C. Domínguez, E. Mata, and V. Pascual. GelJ – a tool for analyzing DNA fingerprint gel images. BMC Bioinformatics 2015, 16:270 http://doi.org/10.1186/s12859-015-0703-0. You can see more information about GelJ in https://sourceforge.net/p/gelj/wiki/Home/ Several videos explaining the use of GelJ are available in https://sourceforge.net/p/gelj/wiki/Videos/ Please address any question or comment to joheras at gmail.com -
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The Kinetic Simulation Algorithm Ontology (KiSAO; http://co.mbine.org/standards/kisao) is an ontology of algorithms for simulating and analyzing biological models, as well as the characteristics of these algorithms, their input parameters, and their outputs. In addition, KiSAO captures relationships among algorithms, their parameters, and their outputs. Development of KiSAO has moved to https://github.com/SED-ML/KiSAO/.
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DigiOz .NET Portal
ASP.NET MVC Based Portal CMS System to Create an Instant Website
DigiOz .NET Portal is a FREE web based portal CMS system written in ASP.NET MVC 5 in C# which uses a Microsoft SQL Database to allows webmasters to setup and customize an instant website for either business or personal use. List of Technologies used: - ASP.NET MVC 5 - Microsoft SQL Server - Bootstrap - HTML 5 - jQuery Demo Site: http://digioznetportal.digioz.net/ Source Code: https://sourceforge.net/p/digioznetportal/codenew/ci/master/tree/ Installation Instructions: https://sourceforge.net/p/digioznetportal/wiki/Home/ Help Wanted: If you are a developer, and wish to join the project, please email us at support@digioz.com. -
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COHCAP
City of Hope CpG Island Analysis Pipeline
COHCAP (City of Hope CpG Island Analysis Pipeline, pronounced "co-cap") is an algorithm to analyze single-nucleotide resolution methylation data (Illumina 450k methylation array, targeted BS-Seq, etc.). Please note: 1) The SourceForge version of COHCAP is no longer being updated. Please see the GitHub version: https://github.com/cwarden45/COHCAP This was the source repository for the Bioconductor version, with some changes after the decision to only provide the code through GitHub. 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) Custom Annotation Files (including EPIC Array): https://sourceforge.net/projects/cohcap/files/additional_Bioconductor_annotations.zip/download -
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AntibiogramJ
AntibiogramJ is a Java program for the reading of antibiogram-images
...Pascual, C. Torres, and M. Zarazaga. AntibiogramJ: a Tool for Analysing Images from Disk Diffusion Tests. Computer Methods and Programs in Biomedicine 143:159-169. 2017. DOI: http://dx.doi.org/10.1016/j.cmpb.2017.03.010 You can see more information about AntibiogramJ in https://sourceforge.net/p/antibiogramj/wiki/Home/ Several videos explaining the use of AntibiogramJ are available in https://sourceforge.net/p/antibiogramj/wiki/Videos/ AntibiogramJ includes now the EUCAST v.9.0. Please address any question or comment to joheras at gmail.com -
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As of 2018-06-28, this project has moved to https://github.com/AdamaJava. This copy of the code will remain but all new code updates and releases will be from the new site. 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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...PLoS ONE 13(2): e0192858. https://doi.org/10.1371/journal.pone.0192858
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BisSNP
Bisulfite-seq/NOMe-seq SNPs & cytosine methylation caller
...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 -
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DualTranscriptDiscovery
Transcript-discovery approach for gene feature delimitation by RNA-seq
http://bio.biologists.org/content/7/1/bio028498 https://www.ncbi.nlm.nih.gov/pubmed/?term=29183907 -
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EFO
The Experimental Factor Ontology describing experimental variables
*** Please note this repository is now deprecated as of January 2018. All EFO development and source code has been moved to https://github.com/EBISPOT/efo *** The Experimental Factor Ontology (EFO) available from http://www.ebi.ac.uk/efo is an application focused ontology modeling the experimental factors in ArrayExpress and constructing mappings to multiple existing domain specific ontologies. To submit new terms, features or report bugs please submit a ticket at the following: http://www.ebi.ac.uk/panda/jira/secure/CreateIssue!... -
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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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detectMITE
Detection of Miniature Inverted Repeat Transposable Elements
...PLoS ONE 9(11): e113349. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0113349 [3] detectMITE user manual Please visit the Wiki page of this website. [4] detectMITE Q&A For Q&A, please visit the Blog page of this website. [5] Update history To see the update history, go to https://sourceforge.net/p/detectmite/wiki/UpdateHistory/ -
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ViralFusionSeq [VFS]
Accurately discover viral integration events and fusion transcripts
VFS was fullly tested under Ubuntu/Debian system. ** Announcement 1**: VFS is superior to Virus-Clip. https://sourceforge.net/projects/viralfusionseq/files/VFS.vs.Virus-Clip.pdf/download As of 2016, VFS is the only viral integration tool available at NIH HPC system. https://hpc.nih.gov/apps/ViralFusionSeq/ ViralFusionSeq (VFS) is a versatile high-throughput sequencing (HTS) tool for discovering viral integration events and reconstruct fusion transcripts at single-base resolution. ... -
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EXCAVATOR2tool
Enhanced tool for detecting CNVs from whole-exome sequencing data
...We recently published on BMC Genomics a novel software package, named XCAVATOR, for the identification of CNVs/CNAs from short and long reads whole-genome sequencing experiments (https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-4137-0). XCAVATOR is freely available at http://sourceforge.net/projects/xcavator/. EXCAVATOR2 is a collection of bash, R and Fortran scripts and codes that analyses Whole Exome Sequencing (WES) data to identify CNVs. EXCAVATOR2 enhances the identification of all genomic CNVs, both overlapping and non-overlapping targeted exons by integrating the analysis of In-targets and Off- targets reads. ... -
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Virtual Cell
Former home of the Virtual Cell platform (VCell), see http://vcell.org
This project and all source code has moved to GitHub, see https://github.com/virtualcell -
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Visualization of Protein-Ligand Graphs
Compute protein graphs. Moved to https://github.com/MolBIFFM/PTGLtools
NOTE: Project moved to https://github.com/MolBIFFM/PTGLtools. The Visualization of Protein-Ligand Graphs (VPLG) software package computes and visualizes protein graphs. It works on the super-secondary structure level and uses the atom coordinates from PDB files and the SSE assignments of the DSSP algorithm. VPLG is command line software. If you do not like typing commands, try our PTGL web server: http://ptgl.uni-frankfurt.de/
