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http://www.xspan.org/

COBrA is a Java-based ontology editor for bio-ontologies that distinguishes itself from other editors by supporting the linking of concepts between two ontologies, and providing sophisticated analysis and verification functions. In addition to the Gene Ontology and Open Biology Ontologies formats, COBrA can import and export ontologies in the Semantic Web formats RDF, RDFS and OWL. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: COBrA (RRID:SCR_005677) Copy   

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http://llama.mshri.on.ca/

The Roth Laboratory is designing and interpreting large-scale experiments to understand pathway structure and its relationship to phenotype and human disease. Software for research focused on a specific research goal is available. Current experimental interests: * Exploiting parallel sequencing technology to phenotype all pairwise gene deletion combinations in S. cerevisiae, with initial application to genes involved in transcription. * Generation of S. cerevisiae strains carrying dozens of chosen targeted deletions, with initial application to delete all ABC transporters imparting multidrug resistance. * Targeted insertion of gene sets encoding entire human pathways into S. cerevisiae, with initial application to genes involved in drug metabolism. Current computational interests: * Systematic analysis of genetic interaction to reveal redundant systems and order of action in genetic pathways * Integrating large-scale studies - including phenotype, genetic epistasis, protein-protein and transcription-regulatory interactions and sequence patterns - to quantitatively assign function to genes and guide experimentation and disease association studies. * Alternative splicing and its relationship to protein interaction networks.

Proper citation: Roth Laboratory (RRID:SCR_005711) Copy   

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http://sourceforge.net/projects/netclassr/

An R package for network-based feature (gene) selection for biomarkers discovery via integrating biological information. The package adapts the following 5 algorithms for classifying and predicting gene expression data using prior knowledge: # average gene expression of pathway (aep); # pathway activities classification (PAC); # Hub network classification (hubc); # filter via top ranked genes (FrSVM); # network smoothed t-statistic (stSVM).

Proper citation: netClass (RRID:SCR_005672) Copy   

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http://web.pacific.edu/

Private Methodist affiliated university with its main campus in Stockton, California, and graduate campuses in San Francisco and Sacramento.

Proper citation: University of Pacific; California; USA (RRID:SCR_005706) Copy   

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http://dbbb.georgetown.edu/research/bioinformatics/

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016.

Proper citation: GUMC Department of Biostatistics Bioinformatics and Biomathematics - Liu Lab (RRID:SCR_005708) Copy   

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http://genemania.org/

Data analysis service to predict the function of your favorite genes and gene sets. Indexing 1,421 association networks containing 266,984,699 interactions mapped to 155,238 genes from 7 organisms. GeneMANIA interaction networks are available for download in plain text format. GeneMANIA finds other genes that are related to a set of input genes, using a very large set of functional association data. Association data include protein and genetic interactions, pathways, co-expression, co-localization and protein domain similarity. You can use GeneMANIA to find new members of a pathway or complex, find additional genes you may have missed in your screen or find new genes with a specific function, such as protein kinases. Your question is defined by the set of genes you input. If members of your gene list make up a protein complex, GeneMANIA will return more potential members of the protein complex. If you enter a gene list, GeneMANIA will return connections between your genes, within the selected datasets. GeneMANIA suggests annotations for genes based on Gene Ontology term enrichment of highly interacting genes with the gene of interest. GeneMANIA is also a gene recommendation system. GeneMANIA is also accessible via a Cytoscape plugin, designed for power users. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: GeneMANIA (RRID:SCR_005709) Copy   

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http://www.bioconductor.org/packages/devel/bioc/html/DMRforPairs.html

Software for identifying differentially methylated regions between unique samples using array based methylation profiles. It allows researchers to compare n greater than or equal to 2 unique samples with regard to their methylation profile. The (pairwise) comparison of n unique single samples distinguishesit from other existing pipelines as these often compare groups of samples in either single CpG locus or region based analysis. DMRforPairs defines regions of interest as genomic ranges with sufficient probes located in close proximity to each other. Probes in one region are optionally annotated to the same functional class(es). Differential methylation is evaluated by comparing the methylation values within each region between individual samples and (if the difference is sufficiently large), testing this difference formally for statistical significance.

Proper citation: DMRforPairs (RRID:SCR_005702) Copy   

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http://www.cincinnatichildrens.org/research/default/

Foundation scientists and physicians conduct breakthrough research to improve care for children as well as train the next generation of investigators. Cincinnati Children's Research Foundation is dedicated to advancing basic, translational, clinical and outcomes-based research. Why choose our cores for your research? We can provide you with cutting-edge, cost-effective technology and data analysis that would be unattainable on an individual research basis. Our fee-for-service program also offers unique studies that you can't find anywhere else. Our faculty also has access to the research cores hosted at the University of Cincinnati College of Medicine. * Animal Behavioral Core * Cardiovascular Imaging Core * Cell Manipulations Laboratory * Cell Processing Core * Cincinnati Biobank * Cincinnati Center for Nutritional Research and Analysis * Comprehensive Mouse and Cancer Core * Gene Expression Microarray Core * Genetic Variation and Gene Discovery Core * Imaging Research Center * Laser Capture Microdissection Microscopy * Lenti-shRNA Library Core * Pathology Research Core * Pluripotent Stem Cell Facility * Research Flow Cytometry Core * Stem Cell Processing Core Lab * Transgenic and Gene Targeting Core * Translational Core Labs * Translational Trials Development and Support Laboratory (TTDSL) * Vector Production Facility * Veterinary Services * Viral Vector Core Support Services: We provide expert consultation, including grant proposal design, data management and regulatory compliance, to investigators at Cincinnati Children's. Research Education and Training: The Cincinnati Children's Research Foundation offers research-based education and training options for scientists, often in conjunction with the University of Cincinnati. High School Programs, Undergraduate Programs, Graduate Degree Programs, Medical Student Program, Postgraduate Programs, Postdoctoral Programs

Proper citation: Research at Cincinnati Childrens (RRID:SCR_005703) Copy   

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http://estbioinfo.stat.ub.es/?page_id=2

The Statistics and Bioinformatics research group has as its main objectives the development of methods and tools to deal with problems appearing in the interface between Statistics and Bioinformatics. We started focusing in DNA microarrays but we are also interested in statistical methods for ''omics'' data integration and next generation sequencing (NGS). Our group collaborates with different research groups in the fields of biology and biomedicine, to whom it offers statistical support for problems which are specifically statistic in nature, such as experimental design or microarray data analysis, and also in more general aspects, such as modeling, analysis or data mining. After a first period of collaboration agreements with the Fundaci�� Vall d''Hebr��n Institut de Recerca we contributed to the creation of the Statistics and Bioinformatics Unit (UEB) which provides statistical and bioinformatical support to VHIR researchers.

Proper citation: University of Barcelona Statistics and Bioinformatics Research Group (RRID:SCR_005704) Copy   

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http://www.univ-lorraine.fr/

French public university.

Proper citation: University of Lorraine; Lorraine; France (RRID:SCR_005705) Copy   

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http://geneontology.svn.sourceforge.net/viewvc/geneontology/go-moose/

go-moose is intended as a replacement for the aging go-perl and go-db-perl Perl libraries. It is written using the object oriented Moose libraries. It can be used for performing a number of analyses on GO data, including the remapping of GO annotations to a selected subset of GO terms. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: go-moose (RRID:SCR_005666) Copy   

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http://www.molgen.de

The research of the group concentrates on the molecular biology of Gram-positive bacteria, with Bacillus subtilis and Lactococcus lactis as the main model organisms. A number of important (human) pathogens are also investigated: Bacillus cereus, Streptococcus pneumoniae and Enterococcus faecalis. The nature of the research is both fundamental and application-oriented. Transcript- and protein profiling by high-throughput technologies such as DNA microarrays and proteomics tools are being used. The very large data sets generated are analyzed by employing existing and novel bioinformatics tools. Major lines of research are in the field of functional genomics of these organisms, using systems- and synthetic biology approaches.

Proper citation: MolGen (RRID:SCR_005700) Copy   

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http://ki.se/ki/jsp/polopoly.jsp?d=29354&a=31610&l=en

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. KI Biobank - Gallstone aims at investigating genetics of gallstone disease on Swedish Twins. Types of samples * EDTA whole blood * DNA * Plasma Number of sample donors: 82

Proper citation: KI Biobank (RRID:SCR_005664) Copy   

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http://www.drugabuse.gov/news-events/podcasts

Audio clips that highlight research efforts at the National Institute on Drug Abuse and include interviews with prominent NIDA scientists. To listen to these clips, just click Listen Now under the clip summary. You must have Real Media Player or Windows Media Player installed to download these clips. To view a printable transcript of a clip, click View Transcript under the clip summary.

Proper citation: NIDA Podcasts (RRID:SCR_005660) Copy   

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http://bmir.stanford.edu/

Mark Musen''s laboratory studies components for building knowledge-based systems, controlled terminologies and ontologies, and technology for the Semantic Web. For more than two decades, Musen''s group has worked to elucidate reusable building blocks of intelligent systems, and to develop scalable computational architectures for systems with significant applications in biomedicine. Informatics is the study of information: its structure, its communication, and its use. As society becomes increasingly information intensive, the need to understand, create, and apply new methods for modeling, managing, and acquiring information has never been greater especially in biomedicine. BMIR is home to world class scientists and trainees developing cutting-edge ways to acquire, represent, process, and manage knowledge and data related to health, health care, and the biomedical sciences. Our faculty, students, and staff are committed to ensuring the biomedical community is properly equipped for the information age, and believe our efforts will provide the structure for the burgeoning revolution of health care and the biomedical sciences.

Proper citation: Stanford Center for Biomedical Informatics Research (RRID:SCR_005698) Copy   

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http://www.bscs.org/science-mental-illness

A set of lessons for students used to gain insight into the biological basis of mental illnesses and how scientific evidence and research can help us understand its causes and lead to treatments and, ultimately, cures. Both the Web version and the free supplement are available. It is a creative, inquiry-based instruction program designed to promote active learning and stimulate student interest in medical topics. This curriculum supplement aims to help students experience the process of scientific inquiry and develop an enhanced understanding of the nature and methods of science.

Proper citation: Science of Mental Illness: Grades 6- 8 (RRID:SCR_005612) Copy   

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http://www.genexplain.com/

An online toolbox and workflow management system for a broad range of bioinformatic and systems biology applications. The individual modules, or Bricks, are unified under a standardized interface, with a consistent look-and-feel and can flexibly be put together to comprehensive workflows. The workflow management is intuitively handled through a simple drag-and-drop system. With this system, you can edit the predefined workflows or compose your own workflows from scratch. Your own Bricks can easily be added as scripts or plug-ins and can be used in combination with pre-existing analyses. GeneXplain GmbH provides a number of state-of-the-art bricks; some of them can be obtained free of charge, while others require licensing for small fee in order to guarantee active maintenance and dynamic adaptation to the rapidly developing know-how in this field.

Proper citation: geneXplain (RRID:SCR_005573) Copy   

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http://bioinfo.unice.fr/

Virtual Biology Lab portal from the University of Nice Sophia Antipolis; Nice; France. Offered are a variety of software including: * GenBank2Treedyn: Extract annotations from GenBank files for: ** More convenient alignments and phylogeny (replace def line of fasta file by GI number) ** Extremely powerful annotations of phylogenetic trees with TreeDyn. * THEA: Analyses of DNA chip data with ontologies * Blast2Tree: Blast server for the identification of procaryotes * Dashboard: e-Tool for data exchanges among partners, DNA chips design and developement * Oligo Heat Map: Check thermodynamical parameters for PCR primers and compute graphical representation to show specificity of target sequences * EmblEx: A cgi tool to parse and extract data from EMBL entries to various formats * Miscellaneous software ** Jane plugin: Add a small panel to Jane server to retrieve PMID of publications ** EtBlast plugin: Add a small panel to EtBlast server to retrieve PMID of publications ** Oligo Builder: Get the oligomers from a set of target sequences by avoiding non-target sequences

Proper citation: Virtual Biology Lab (RRID:SCR_005694) Copy   

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https://biit.cs.ut.ee/

The Bioinformatics, Algorithmics, and Data Mining group BIIT lead by prof. Jaak Vilo is a joint research group between the Department of Computer Science (University of Tartu), Quretec, and the Estonian Biocenter. Our main research topics and capabilities include the gene regulation, gene expression data analysis, biological data mining, systems biology, combinatorial pattern matching, developing software for biomedical research databases, as well as partnering in stem cell and cancer related projects. Software * MEM - Multi-Experiment-Matrix -- large-scale gene expression data queries and mining (Genome Biology 2009) * g:Profiler family of tools for functional assessment of gene groups, gene ID mappings, orthology and expression similarity searches. (NAR web server issue 2007) * KEGGanim - visualisation of high-throughput data on biological pathway charts (Bioinformatics, 2007) * GraphWeb - a tool for mining large biological networks (NAR Web server issue 2008) * FunGenES data atlas * More software tools

Proper citation: BIIT - Bioinformatics Algorithmics and Data Mining Group (RRID:SCR_005690) Copy   

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http://www.cipf.es/

The Pr��ncipe Felipe Research Centre (CIPF), which was inaugurated by their Royal Highnesses the Prince and Princess of Asturias on 17th March 2005, is a centre dedicated to biomedical research, with the aim of taking on new challenges in the field of basic research and encouraging scientific works of excellence. The construction of the Centre was carried out thanks to the Regional Development Funds from the European Union, and from the Regional Government (Generalitat Valenciana) through its Ministry of Health. The current financing of the CIPF comes mainly from the investment made by the Generalitat Valenciana through the Ministry of Health, as well as the Regenerative Medicine Programme, the fruit of an agreement between the Institute of Health Carlos III and the Ministry of Health for basic and translation research in this field. The CIPF takes the research tradition from the then Valencian Cytological Research Institute and the Valencian Biomedical Research Foundation, with the aim of consolidating and expanding this research. Therefore the activity in the CIPF can be divided into three main strategic work areas: The Regenerative Medicine area focuses its research on cellular therapy and interdisciplinary research in human embryonic and adult stem cells, with the aim of regenerating damaged organs to improve human health. The Chemical and Quantative Biology area aims to understand, through the application of (bio) chemical, genetic, and bioinformatic methods, to understand the molecular mechanisms that control the biological processes and alterations that lead to pathological conditions. The Biomedicine area focuses on understanding the molecular bases of human pathologies that require new diagnostic and clinical procedures for their identification and treatment, pathologies such as cancer, neurological pathologies and rare illnesses.

Proper citation: Principe Felipe Research Centre; Valencia; Spain (RRID:SCR_005691) Copy   

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