|APECS||Apex Peptide Elution Chain Selection (APECS) is a proteomics method for intensity-based precursor ion selection, using a MALDI-TOF/TOF instrument, from a complex sample separated by 2D-LC.||0 developers|
|ASCA||Identifying factors influencing complex proteomics profile using factorial design and ANOVA – simultaneous component analysis.||1 developer|
|biobanking||Generic code and mailing lists for the biobanking task force.||4 developers|
|BiomarkerFeatureSelection||This project contains Matlab code of feature selection algorithms to identify biomarker candidates in pre-processed LC-MS data. It also contains two pre-processed LC-MS data sets with annotation of spiked-in peptides. Code and data sets are used in article "A critical assessment of feature selection methods for biomarker discovery in clinical proteomics" under revision at Molecular & Cellular Proteomics.||1 developer|
|biosemantics||Support of researchers and developers working on semantic solutions for life science projects.||12 developers|
|brs2011p07||A collection of Cytoscape plugins to import spreadsheets, plot node/edge attributes and create subnetworks for disconnected graphs.||4 developers|
|BRSP200901_VanPassel||A pangenomic acquisition account of genomic islands in prokaryotes||0 developers|
|BRSP201017||Spectral Tree Viewer visualize MultiMultistage Mass Spectrometry data in a browser.||5 developers|
|COMPANION||Comparative Annotation of bacterial genomes.||3 developers|
|compendiumAnalysis||An R package for the analysis of the compendium of microarray datasets||1 developer|
|ConceptProfileMiningWS||Code for the Concept Profile Mining Webservices.||5 developers|
|ConceptRewrite||A frontend built to search, edit and create concepts for ConceptWiki||4 developers|
|conceptweb||Code and communications platform for the Concept Web Alliance||2 developers|
|conceptwiki||A universal open access repository of editable concepts. This is part of Open PHACTS.||15 developers|
|conerice||Configuration files and documentation for bioinformatics servers/services.||8 developers|
|cw-api-client||A generic ConceptWiki API client for Java/Groovy applications||4 developers|
|cytoscaperpc||An RPC plugin for Cytoscape RPC that allows XML-RPC clients to query and change attributes in Cytoscape. This makes it possible to use Cytoscape as an external visualization platform without constantly in- and exporting data.||2 developers|
|daf||Data Analysis Framework that enables any computer program (i.e proteomics tools) to run on a Distributed Computing environment (Grid, Cloud, Cluster, Lightpath etc.). DAF provides Web Services to the end user.||3 developers|
|dafportal||A Web Portal providing data analysis services for Life Science data using tools integrated in DAF. The portal is written using Dojo Toolkit while REST/HTTP base Web Services client written in PHP.||3 developers|
|data-mining||Automatically recognizing concepts in human-readable text. This project uses Peregrine as text indexer. It searches for known terms in an input text and maps them to concepts in an ontology. If a term could refer to more than one concept then Peregrine tries to disambiguate it.||9 developers|
|db-iga||Double Boundary Iterative Group Analysis; used to test whether groups of annotated items (e.g. genes) are significantly clustered in a ranked list.||0 developers|
|dbnp-metagenomics||Metagenomics module for the Generic Study Capturing Framework (gscf) within dbNP.||1 developer|
|DEmARC||DEmARC is an R package for hierarchical classification of viral genomes based on multiple alignments of strongly conserved proteins. Classification is typically done on the virus family level, and quantitative support is given for both the ranks and the taxa of the classification. Different types of plots are provided for visual inspection and interpretation of the results. The methodology might be useful for the analysis of cellular organisms as well.||1 developer|
|DISC||Mailing lists for the Data integration and stewardship centre||1 developer|
|DVD||Diagnostic Variant Database (DVD) is used to share all genetic variants detected in the course of next-generation sequencing (NGS) applications between collaborators.||4 developers|
|e-biobank||involves building a model infrastructure for the Dutch Biobank community, BBMRI-NL, that manages resources for the future of biomedical research. It forms a hub in the European Biobanking and Biomolecular Resources Research Infrastructure.||10 developers|
|elabfactory||Generic code and mailing lists for those involved in developing e-Laboratory components in the context of NBIC's BioAssist project.||11 developers|
|essentials||High-throughput analysis of genome-wide transposon mutant libraries is a powerful tool for (conditional) essential gene discovery. Recently, several next generation sequencing approaches, e.g. Tn-seq, INseq and TraDIS, have been developed that accurately map the site of transposon insertions by mutant-specific amplification and sequence readout of DNA flanking the transposon insertions site, assigning a measure of essentiality based on the number of reads per gene or per mutant. However, analysis of these large and complex datasets is hampered by the lack of an easy to use and automated tool for transposon insertion sequencing data.
To fill this gap, we developed ESSENTIALS, an open source, web-based software tool for researchers in the genomics field utilizing transposon insertion sequencing analysis. It accurately predicts (conditionally) essential genes and offers the flexibility of using different sample normalization methods, genomic location bias correction, data preprocessing steps, appropriate statistical tests and various visualizations to examine the results, while requiring only a minimum of input and hands-on work from the researcher.
We successfully applied ESSENTIALS to in-house and published Tn-seq, TraDIS and HITS datasets and we show that the various pre- and post-processing steps on the sequence reads and count data with ESSENTIALS markedly improve the sensitivity and specificity of predicted gene essentiality.
|fgweb||A web-interface that allows to integrate functional genomics data and bioinformatic tool flows with a minimum of time investment in robust web-based software.||4 developers|
|fluxes||A program for metabolic flux analysis using NMR spectra of tracer experiments. It allows assembling model equations for arbitrary metabolic systems using a simple input format.||1 developer|
|foundation||Project for the setup of a foundation for the governance of open source software in a bioinformatics context; software that is not used by programmers; software for which the governance requires a community of users (life-scientists, biologists, clinicians, laboratory personnel, etc) as well as a community of programmers (bioinformaticians, informaticians, statisticians, etc)||7 developers|
|galaxytools||Tools developed by various groups in the BioAssist platforms together with their tool configs for installation in a Galaxy server.||29 developers|
|gonl||The Genome of the Netherlands||5 developers|
|hope||An easy-to-use webserver that analyses the structural effects of protein point mutations. Project HOPE collects and combines available information from a series of webservers and databases to produce a mutation report complete with results, figures and animations.||1 developer|
|ibb||An R package for the (inverted) beta binomial test for count data||1 developer|
|ibidas||A database program designed to store all kinds of biological data. A very generic data scheme and command line access through Python are two of the highlights.||2 developers|
|inspecter||Retrieval, filtering, integration, scoring and visualization of proteomics data as stored in the PRIDE repository database.||0 developers|
|interoperability||Generic code and mailing lists for the NBIC BioAssist interoperability task force.||14 developers|
|InterProScan_Grid||A package to submit InterproScan 5 jobs to the Duthc lifescience grid.
We us e PiCas for Job management.
|JAG||Joint Action of Genes||4 developers|
|LCMS_time_alignment_algorithms||Container of several different time alignment algorithms developed for LC-MS such as Correlation Optimized Warping, Dynamic Time Warping and Parametric Time Warping using preselected mass traces with COmponent Detection Algorithm (COW-CODA, DTW-CODA and PTW-CODA).||2 developers|
|LineUp||Cytoscape plugin for comparing gene expression in a network context||1 developer|
|linker||A web based user interface ("Knowledge Enhancer") using semantic technology to create a popup in the browser linking terms in the text to concepts in the ConceptWiki and other third party services. Aimed at knowledge discovery.||9 developers|
|loft||An implementation of "Levels of Orthology through Phylogenetic Trees"||1 developer|
|lysndenovo||Prototype implementation of LysNDeNovo algorithm for peptide sequencing of MS2 ETD spectra.||2 developers|
|mariboes||MaRIboES is a system for metabolite and reaction inference based on enzyme specificities. It employs structural and stereochemistry similarity measures and molecular fingerprints to generalise enzymatic reactions based on data available in BRENDA.||1 developer|
|MassComb||Proteomics: tools and wrappers for X! Tandem and mzidentml-parsers.||2 developers|
|maxpc||MaxAPC takes as input IMPUTE/SNPTEST .gen and .sample files. On the basis of these two file statistics are calculated and provided in the two outputfiles:
1.) the maximum, average, posterior call averaged per individual (one average per individual) - .pi file.
2.) the maximum, average, posterior call averaged per SNP (one average per SNP) - .ps file.
|meta||Metaproject: a source for information on using the development environment and to report problems.||3 developers|
|metabo-conv||This application is officially programmed to up-load human metabolic pathway data from KEGG, Reactome, HumanCyc, and WikiPathways to a data warehouse. Such a data warehouse can be used to compare data across the uploaded databases. This way high similar reactions can be retrieved. Such results can offer a valuable source for a reconciliation of metabolic pathway data. A unified data model has been used that treats extracted data from any metabolic pathway database equally. Therefore addition of new metabolic pathway data is relatively easy.||1 developer|
|metidb||Search through a database or predicted NMR spectra for small compounds in a variety of ways to identify the compound in your NMR spectrum. Implemented with Java, Hibernate, Spring & Wicket.||4 developers|
|molgenis||Quickly and automatically generate databases and rich user interfaces to track and trace all your research data. Integrate with your analysis tools in R, Java and web services. See http://www.molgenis.org/ for more details.||1 developer|
|msCompare||Framework for the analysis of label-free LC-MS data for comparative profiling studies||4 developers|
|Multi-netclust||Multi-netclust is a simple tool that allows users to extract connected clusters of data represented by different networks given in the form of matrices.
Arnold Kuzniar, Somdutta Dhir, Harm Nijveen, Sándor Pongor, and Jack A.M. Leunissen
Multi-netclust: an efficient tool for finding connected clusters in multi-parametric networks
Bioinformatics (2010) 26(19): 2482-2483 first published online August 2, 2010 doi:10.1093/bioinformatics/btq435
|mzcms||A lightweight CMS for proteomics results||1 developer|
|NARWHAL||a primary analysis pipeline for NGS data||3 developers|
|nbic2014||Organization project for the NBIC2014 conference||2 developers|
|nbiceng||Generic code and mailing lists for the BioAssist Engineering Team||9 developers|
|nbicgalaxy||A hosting place for documents, discussions, bug reports on NBIC Galaxy Server||7 developers|
|netbeans-presentation||Example code for the presentation on Netbeans at the BioAssist Programmer's Meeting of January 13th, 2012||1 developer|
|ngstools||This project contains the source code developed within the NGS task force.||2 developers|
|npclib||Mass Spectrometry Java Data Models
The project consists of a library of java classes that describe the most common data models used in mass spectrometry.
|nugoctdwebapp||NuGO Clean Transcriptome Database Webapp
Webapplication for the NuGO blackboxes for processing CEL-files into a 'NuGO clean transcriptome database'.
|omimparser||A parser for the OMIM database to extract the mutation of allelic variant on AA and nucleotide level.||1 developer|
|OPF||Overlapping Peak Finder is a Java program that deconvolutes overlapping isotopic clusters based on an isotopic distribution prediction algorithm.
It can be used as a post-processing tool to correct the results obtained by common quantification software.
|opl||Code repository for researchers/developers at the OncoProteomics Lab, Cancer Center Amsterdam, VU University Medical Center.||1 developer|
|Panter||Panter stands for the Persons and Address Informationsystem NTR. Panter provides a user interface to the address and research administration database of the Netherlands Twin Register. The application is written in C# and uses an MS-SQL server as database store. An open source edition is provided here under the GPLv3 license.||1 developer|
|PASSion||PASSion: a pattern growth based algorithm for splice site detection from paired-end RNA-Seq reads.||3 developers|
|PhenoLink||PhenoLink allows linking phenotypes to large ~omics data sets, which is essential for generating leads to understand the underlying mechanism of a phenotype. It pre-processes input data to decrease noise and uses the Random Forest algorithm for feature selection to accurately find features that are linked to phenotypes. Additionally, the PhenoLink provides visualization of links that allows quick identification of relations (i) between features and phenotypes, (ii) among features, (iii) among phenotypes, and (iv) features and organisms, which use different feature sets to exhibit the same phenotype.||3 developers|
|pICalculator||A java pI calculator as described in the article Proteomics 2008, 8, 4898–4906. "A versatile peptide pI calculator for phosphorylated and N-terminal acetylated peptides experimentally tested using peptide isoelectric focusing". Sharon Gauci, Bas van Breukelen, Simone M. Lemeer, Jeroen Krijgsveld and Albert J. R. Heck.||1 developer|
|PiCaS||A Python framework to generate grid output servers||1 developer|
|Pindel||Pindel: a pattern growth approach to detect break points of large deletions , medium sized insertions, inversions and other structural variations from paired-end short reads.||13 developers|
|PipelineFunctionalRequirements||A list of Bioinformatics pipelines used together with descriptions of what technologies are used, which tools, which I/Os, etc.
The goal is to capture functional requirements to be used as feedback by existing workflow/pipeline technologies.
|Pre-alignment||Time alignment for complex LC-MS datasets typically obtained from inter-laboratory studies. The developed application allows retention time alignment of diverse LC-MS datasets by first accurately identifying peak correspondences using Bi-variate 2D Kernel density estimation and then extracting a non-linear monotonic regression function from the retention time co-ordinates of these peak correspondences.||3 developers|
|proteomics||Generic code and mailing lists for researchers and developers working in the BioAssist proteomics task force.||12 developers|
|pview-cli||This project adds a command line interface (cli) to pview (see compbio.cs.princeton.edu/pview).||4 developers|
|QualitySNP||QualitySNPng: a user-friendly SNP detection and visualization tool
Published in the NAR Webserver issue:
|RGPU||A programmer-friendly package to help "R" programmers use processing on a video card to speedup bioinformatics analysis with R by a factor larger than 50.||1 developer|
|rite||The packages in rite form a pilot job framework written purely in Java. MongoDB is used as storage for job descriptions.||1 developer|
|rockerbox||A cross-platform JAVA GUI application for filtering low quality peptide-spectrum matches (PSMs) and charting from Mascot (.dat) output files, based on user-defined criteria or automatically for a target FDR.||1 developer|
|RoVar||Robust Variant detection in genome sequences using Next Generation Data from various platforms||2 developers|
|sandbox||Sandbox project for NBIC project developers. If you want to experiment with the tools at your disposal, please do it here.||5 developers|
|SDisc||An automated subtyping methodology in R designed to facilitate the search for homogeneous subtypes in clinical studies.||1 developer|
|SedMat||Proteomics: single experiment matching tool.||2 developers|
|SKOSVocabularyEditor||A graphical editor for SKOS Vocabularies.||4 developers|
|Solid_XSQ_converter||A java tool to convert Solid XSQ files to BWA specific CSFastQ files. More output options will be added.
Uses the http://www.hdfgroup.org/hdf-java-html/ library. Make sure to download their native c++ HDF5 libraries and to put them somehwere on the Java path.
|statquant||A post quantification analysis toolbox for improving quantitative mass spectrometry||2 developers|
|stormy-ws||Cloud based webservice failover.||2 developers|
|sysadmin||General system administration scripts used by the BioAssist Engineering Team||6 developers|
|trait-ngs||Project management repository for the NGS work package of the CTMM TraIT project. For internal use only.||10 developers|
|wikidata||A web site application that stores knowledge and information using concept triples. Users can both view and edit the contents of the triple store using a wiki-like application.||11 developers|
|WISECONDOR||WIthin-SamplE COpy Number aberration DetectOR.
Reliable High Resolution Non-Invasive Fetal DNA Sequence Analysis Using Shallow Next Generation Sequencing.