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http://cvm.msu.edu/

The college includes four biomedical science departments -- microbiology and molecular genetics, pathobiology and diagnostic investigation, pharmacology and toxicology, and physiology; two clinical departments -- large-animal clinical sciences and small-animal clinical sciences; two service units -- the Veterinary Teaching Hospital and the Diagnostic Center for Population and Animal Health; and several research centers. In addition to the Doctor of Veterinary Medicine degree program, the college also offers certificate and bachelors degree programs in veterinary technology, as well as advanced degree (masters and doctor of philosophy) programs. The mission of the College of Veterinary Medicine is to develop a diverse academic community that fosters scholarly activity and encourages exemplary human qualities in order that the art and science of veterinary medicine may be imparted to students, expanded by research, and extended to the public for the benefit of animal and human health to meet the changing needs of Michigan, the nation, and the world. The College of Veterinary Medicine is fortunate to have an outstanding faculty, all of whom hold the doctor of veterinary medicine degree and/or the doctor of philosophy degree. Nearly all of the specialty boards recognized by the American Veterinary Medical Association are represented on the faculty. Many of these faculty members are leaders in their fields, both nationally and internationally. Michigan State has a long-standing commitment to equal opportunity, affirmative action, and multiculturalism. The College of Veterinary Medicine has attained national recognition for its leadership in programs for the encouragement of underrepresented groups at the preprofessional, professional, and advanced studies levels, as well as for increased diversity in its faculty. Special opportunities for preveterinary and professional students to participate in international veterinary activities further expand appreciation of different cultures. Indeed, international experience and opportunities abound in the college for both faculty and students. Nearly 300 individuals associated with the college have been involved in activities in 36 countries. A special endowment provides funds to support student travel abroad. The abundance and variety of animal agriculture and companion animals in Michigan provides the college with one of the largest clinical and diagnostic caseloads in the country. Educational and research opportunities are considerably enhanced by this large caseload. The college also takes seriously its obligation to meet the needs of society in addition to clinical services and education. The college has expertise in public health, biomedical and comparative medical research, ecosystem and environmental management, and the multiple facets that compose our complex global food system. CVM also supports key animal health programs conducted by both the Michigan Department of Agriculture and the U.S. Department of Agriculture.

Proper citation: Michigan State University College of Veterinary Medicine (RRID:SCR_012848) Copy   

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http://bioinfo2.ugr.es/NGSmethDB/

A dedicated database for the storage, browsing and data mining of whole-genome, single-base-pair resolution methylomes.

Proper citation: NGSmethDB (RRID:SCR_012847) Copy   

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http://genomeview.org/

A next-generation stand-alone genome browser and editor initiated in the BSB group at VIB and currently developed at Broad Institute.

Proper citation: GenomeView (RRID:SCR_012968) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/seqminer/

Software for a genome wide mapping data interpretation platform for NGS (ChIPSeq).

Proper citation: seqMINER (RRID:SCR_013020) Copy   

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http://sourceforge.net/projects/mireap/

A software tool which can be used to identify both known and novel microRNAs from small RNA libraries deeply sequenced by Solexa/454/Solid technology.

Proper citation: MIREAP (RRID:SCR_013025) Copy   

•   Source: SciCrunch Registry
  

http://www.lgm.upmc.fr/mirena/index.html

A software tool to find microRNAs with high accuracy and no learning at genome scale and from deep sequencing data.

Proper citation: MIReNA (RRID:SCR_013024) Copy   

•   Source: SciCrunch Registry
  

https://mig.molbiol.ox.ac.uk/mig/

Allows the user to conveniently compare data from many loci., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: MIG (RRID:SCR_012972) Copy   

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http://www.bioconductor.org/packages/release/bioc/html/charm.html

Function for differentially methylated regions (DMR) detection that is a part of the charm package in R/Bioconductor.

Proper citation: dmrFinder (RRID:SCR_012853) Copy   

•   Source: SciCrunch Registry
  

http://www.cdc.gov/brfss

The Behavioral Risk Factor Surveillance System (BRFSS) is a state-based system of health surveys that collects information on health risk behaviors, preventive health practices, and health care access primarily related to chronic disease and injury. For many states, the BRFSS is the only available source of timely, accurate data on health-related behaviors. BRFSS was established in 1984 by the Centers for Disease Control and Prevention (CDC); currently data are collected monthly in all 50 states, the District of Columbia, Puerto Rico, the U.S. Virgin Islands, and Guam. More than 350,000 adults are interviewed each year, making the BRFSS the largest telephone health survey in the world. States use BRFSS data to identify emerging health problems, establish and track health objectives, and develop and evaluate public health policies and programs. Many states also use BRFSS data to support health-related legislative efforts. Sponsors: This resource is supported by the Center for Disease Control. Keywords: Behavioral, Risk, Factor, Surveillance, System, Health, Disease, Chronic, Injury, Health, Behavior, Health,

Proper citation: Behavioral Risk Factor Surveillance System (RRID:SCR_012974) Copy   

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https://darlinglab.org/mauve/mauve.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software as system for efficiently constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion.

Proper citation: Mauve (RRID:SCR_012852) Copy   

•   Source: SciCrunch Registry
  

http://www.djangoproject.com/

Django is a high-level Python Web framework that encourages rapid development and clean, pragmatic design. Developed four years ago by a fast-moving online-news operation, Django was designed to handle two challenges: the intensive deadlines of a newsroom and the stringent requirements of the experienced Web developers who wrote it. It lets you build high-performing, elegant Web applications quickly. Django focuses on automating as much as possible and adhering to the DRY principle.

Proper citation: Django (RRID:SCR_012855) Copy   

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http://www.nidcd.nih.gov/

The National Institute on Deafness and Other Communication Disorders (NIDCD) is one of the Institutes that comprise the National Institutes of Health (NIH). Established in 1988, NIDCD is mandated to conduct and support biomedical and behavioral research and research training in the normal and disordered processes of hearing, balance, smell, taste, voice, speech, and language. The Institute also conducts and supports research and research training related to disease prevention and health promotion; addresses special biomedical and behavioral problems associated with people who have communication impairments or disorders; and supports efforts to create devices which substitute for lost and impaired sensory and communication function. It is estimated that more than 46 million people in the United States suffer some form of disordered communication. NIDCD has focused national attention on disorders of human communication and has contributed to advances in biomedical and behavioral research that will improve the lives of millions of individuals with communication disorders. NIDCD has made important contributions to the body of knowledge needed to help those who experience communication disorders and to advance research in all aspects of human communication. NIDCD accomplishes its mandate through the Division of Intramural Research, which conducts research in laboratories at the NIH, and the Extramural Research Program, a program of research grants, career development awards, individual and institutional research training awards, center grants, and contracts to public and private research institutions and organizations. As a whole, the Institute supports and conducts approximately 600 research projects. The Institute also conducts and supports research and research training in disease prevention and health promotion and the special biomedical and behavioral problems associated with people having communication impairments and disorders. NIDCD''s extramural grant portfolio demonstrates a balance of basic and clinical research. The intramural research program spans a variety of topics, including, but not limited to, the development of a vaccine against otitis media, the identification and characterization of genes responsible for hereditary hearing impairment, genes associated with neoplasms affecting human communication, and treatment of voice disorders.

Proper citation: National Institute on Deafness and Other Communication Disorders (RRID:SCR_012859) Copy   

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http://sourceforge.net/projects/msa-edna/

Software for Multiple Sequence Alignment for Transcription Factor Binding Sites using Di nucleotides dependencies and relying on Free Interaction energies between neighbouring DNA bases to stabilise substitution energy of the alignment.

Proper citation: EDNA (RRID:SCR_012981) Copy   

•   Source: SciCrunch Registry
  

http://bioconductor.org/packages/2.12/bioc/html/cn.mops.html

A data processing pipeline for copy number variations and aberrations (CNVs and CNAs) from next generation sequencing (NGS) data.

Proper citation: cn.mops (RRID:SCR_013036) Copy   

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http://sourceforge.net/projects/samzip/

An encoding and decoding tool for Sequence Alignment/Map (SAM) files.

Proper citation: SAMZIP (RRID:SCR_012980) Copy   

•   Source: SciCrunch Registry
  

Ratings or validation data are available for this resource

http://ccb.jhu.edu/software/tophat/index.shtml

Software tool for fast and high throughput alignment of shotgun cDNA sequencing reads generated by transcriptomics technologies. Fast splice junction mapper for RNA-Seq reads. Aligns RNA-Seq reads to mammalian-sized genomes using ultra high-throughput short read aligner Bowtie, and then analyzes mapping results to identify splice junctions between exons.TopHat2 is accurate alignment of transcriptomes in presence of insertions, deletions and gene fusions.

Proper citation: TopHat (RRID:SCR_013035) Copy   

•   Source: SciCrunch Registry
  

http://www.viprbrc.org/brc/home.do?decorator=vipr

Provides searchable public repository of genomic, proteomic and other research data for different strains of pathogenic viruses along with suite of tools for analyzing data. Data can be shared, aggregated, analyzed using ViPR tools, and downloaded for local analysis. ViPR is an NIAID-funded resource that support the research of viral pathogens in the NIAID Category A-C Priority Pathogen lists and those causing (re)emerging infectious diseases. It provides a dedicated gateway to SARS-CoV-2 data that integrates data from external sources (GenBank, UniProt, Immune Epitope Database, Protein Data Bank), direct submissions, analysis pipelines and expert curation, and provides a suite of bioinformatics analysis and visualization tools for virology research.

Proper citation: Virus Pathogen Resource (ViPR) (RRID:SCR_012983) Copy   

•   Source: SciCrunch Registry
  

http://sammate.sourceforge.net/

An open source GUI software suite to process RNA-Seq data. It is composed of two modules: assemblySAM and SAMMate.

Proper citation: SAMMate (RRID:SCR_013037) Copy   

•   Source: SciCrunch Registry
  

http://mobyle.pasteur.fr/

A portal for bioinformatics analyses, including the following: alignment assembly database display genetics hmm information nucleic phylogeny protein sequence structure

Proper citation: Mobyle@Pasteur (RRID:SCR_013089) Copy   

•   Source: SciCrunch Registry
  

http://rnai.dkfz.de

GenomeRNAi is a database of phenotypes from systematic RNA interference (RNAi) screens in cultured Drosophila cells. The phenotype database can be searched by keywords, RNAi identifiers or Drosophila gene sequences. Searches with homologous sequences from human or C. elegans are also possible. Integrated tools evaluate the specificity of long double-stranded RNAs (RNAi probes) by similarity searches against all predicted Drosophila transcripts. This site can also be used to identify pre-designed RNAi probes from available Drosophila RNAi libraries. Caenorhabditis elegans genome, human genome

Proper citation: GenomeRNAi (RRID:SCR_013088) Copy   

•   Source: SciCrunch Registry