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http://www.energy.gov/

The mission of the Department of Energy is to ensure America''s security and prosperity by addressing its energy, environmental, and nuclear challenges through transformative science and technology solutions. Goal 1: Transform our Energy Systems - Catalyze the timely, material, and efficient transformation of the nation''s energy system and secure U.S. leadership in clean energy technologies. Goal 2: The Science and Engineering Enterprise - Maintain a vibrant U.S. effort in science and engineering as a cornerstone of our economic prosperity, with clear leadership in strategic areas. Goal 3: Secure Our Nation - Enhance nuclear security through defense, nonproliferation, and environmental efforts. Goal 4: Management and Operational Excellence - Establish an operational and adaptable framework that combines the best wisdom of all Department stakeholders to maximize mission success.

Proper citation: United States Department of Energy (RRID:SCR_012841) Copy   

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http://www.usaid.gov/

Proper citation: USAID (RRID:SCR_012846) Copy   

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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://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

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   

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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://www.bioconductor.org/packages/release/bioc/html/ChIPpeakAnno.html

Software package that includes functions to retrieve the sequences around the peak, obtain enriched Gene Ontology terms, find the nearest gene, exon, miRNA or custom features such as most conserved elements.

Proper citation: ChIPpeakAnno (RRID:SCR_012828) Copy   

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http://mitobreak.portugene.com/cgi-bin/Mitobreak_home.cgi

Database with curated datasets of mitochondrial DNA (mtDNA) rearrangements. Users may submit new mtDNA rearrangements.

Proper citation: MitoBreak (RRID:SCR_012949) Copy   

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http://sourceforge.net/projects/ngsep/

Software whose main functionality is the variants detector, which allows to make simultaneous discovery of SNVs, small indels, and CNVs.Accurate variant calling across species and sequencing protocols.Used for analysis of DNA high throughput sequencing data.

Proper citation: NGSEP (RRID:SCR_012827) Copy   

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

Collection of techniques to remove inter-study bias when combining gene expression data originating from different studies.

Proper citation: inSilicoMerging (RRID:SCR_012829) Copy   

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http://www.rcsb.org/#Category-welcome

Collection of structural data of biological macromolecules. Database of information about 3D structures of large biological molecules, including proteins and nucleic acids. Users can perform queries on data and analyze and visualize results.

Proper citation: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) (RRID:SCR_012820) Copy   

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http://www.sourceforge.net/projects/matcont

MATCONT is a graphical MATLAB package for the interactive numerical study of parameterized dynamical systems. It is developed in parallel with the command line continuation toolbox CL_MATCONT and with the command line continuation toolbox CL_MATCONTM for the interactive numerical study of parameterized maps and iterates of maps. MATCONT and CL_MATCONT allow the numerical continuation of equilibria, limit cycles and homoclinic orbits, detection of codimension 1 and 2 bifurcations, continuation of the codimension 1 bifurcations and computation of their normal forms. For equilibria normal form coefficients of codimension 2 bifurcations are also computed, as well as switching to the codimension 1 curves in codimension 2 points. CL_MATCONTM provides similar facilities for maps and iterates of maps, including normal form coefficients of codimension 2 bifurcations and continuation of homoclinic and heteroclinic connections and tangencies of such connections.

Proper citation: MATCONT and CL MATCONT: Continuation Software in Matlab (RRID:SCR_012822) Copy   

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http://bioconductor.org/packages/release/bioc/html/DEXSeq.html

Software package focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.

Proper citation: DEXSeq (RRID:SCR_012823) Copy   

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http://www.bioconductor.org/packages/2.12/bioc/html/snapCGH.html

Software providing methods for segmenting, normalising and processing aCGH data; including plotting functions for visualising raw and segmented data for individual and multiple arrays.

Proper citation: snapCGH (RRID:SCR_012947) Copy   

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http://www.fda.gov/ScienceResearch/BioinformaticsTools/Arraytrack/default.htm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 23,2023. Provides an integrated solution for managing, analyzing, and interpreting microarray gene expression data.

Proper citation: ArrayTrack (RRID:SCR_012839) Copy   

•   Source: SciCrunch Registry

http://www.cihr-irsc.gc.ca/e/193.html

The Canadian Institutes of Health Research (CIHR) is the Government of Canada''s agency responsible for funding health research in Canada. CIHR was created in 2000 under the authority of the CIHR Act and reports to Parliament through the Minister of Health. CIHR''s budget for 2008-09 is $928.6 million, of which $132 million is allocated to administering the Networks of Centres of Excellence and Canada Research Chair programs. CIHR was created to transform health research in Canada by: * funding more research on targeted priority areas; * building research capacity in under-developed areas such as population health and health services research; * training the next generation of health researchers; and * focusing on knowledge translation, so that the results of research are transformed into policies, practices, procedures, products and services. CIHR consists of 13 virtual institutes, a structure that is unique in the world. These innovative institutes bring together all partners in the research process - the people who fund research, those who carry it out and those who use its results - to share ideas and focus on what Canadians need: good health and the means to prevent disease and fight it when it happens. Each institute supports a broad spectrum of research in its topic areas and, in consultation with its stakeholders, sets priorities for research in those areas.

Proper citation: Canadian Institutes of Health Research (RRID:SCR_012838) Copy   

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

Software tools for analyzing and visualizing Illumina''s 450k array data.

Proper citation: minfi (RRID:SCR_012830) Copy   

•   Source: SciCrunch Registry

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

Software package that provides pathway enrichment techniques for miRNA expression data.

Proper citation: miRNApath (RRID:SCR_012833) Copy   

•   Source: SciCrunch Registry