Active projects

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
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
Biosemantic All source codes for Biosemantic group from Erasmus MC Rotterdam.
Website: biosemantics.org
2 developers
biosemantics Support of researchers and developers working on semantic solutions for life science projects. 14 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
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. 16 developers
conerice Configuration files and documentation for bioinformatics servers/services. 8 developers
ContigLayout 1 developer
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. 10 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. 12 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.
2 developers
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. 15 developers
InterProScan_Grid A package to submit InterproScan 5 jobs to the Duthc lifescience grid.
We us e PiCas for Job management.
1 developer
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.
1 developer
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
metagenomics 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
2 developers
mzcms A lightweight CMS for proteomics results 1 developer
nanopub 4 developers
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 2 developers
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.
3 developers
nugoctdwebapp NuGO Clean Transcriptome Database Webapp

Webapplication for the NuGO blackboxes for processing CEL-files into a 'NuGO clean transcriptome database'.
5 developers
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.
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.
1 developer
pmid2doi 3 developers
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). 5 developers
QualitySNP QualitySNPng: a user-friendly SNP detection and visualization tool

http://www.bioinformatics.nl/QualitySNPng/

Published in the NAR Webserver issue:
http://nar.oxfordjournals.org/content/early/2013/04/29/nar.gkt333.short
1 developer
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.
1 developer
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.
2 developers

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