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http://creskolab.uoregon.edu/stacks/

A software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. It was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography.

Proper citation: Stacks (RRID:SCR_003184) Copy   

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

Software package that provides functions for identification and visualization of potential intramolecular triplex patterns in DNA sequence. The main functionality is to detect the positions of subsequences capable of folding into an intramolecular triplex (H-DNA) in a much larger sequence. The potential H-DNA (triplexes) should be made of as many canonical nucleotide triplets as possible. The package includes visualization showing the exact base-pairing in 1D, 2D or 3D.

Proper citation: Triplex (RRID:SCR_003061) Copy   

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http://purl.bioontology.org/ontology/ICNP

Ontology of the international classification for nursing practice.

Proper citation: International Classification for Nursing Practice (RRID:SCR_003099) Copy   

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http://www.wormbase.org

Central data repository for nematode biology including complete genomic sequence, gene predictions and orthology assignments from range of related nematodes.Data concerning genetics, genomics and biology of C. elegans and related nematodes. Derived from initial ACeDB database of C. elegans genetic and sequence information, WormBase includes genomic, anatomical and functional information of C. elegans, other Caenorhabditis species and other nematodes. Maintains public FTP site where researchers can find many commonly requested files and datasets, WormBase software and prepackaged databases.

Proper citation: WormBase (RRID:SCR_003098) Copy   

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http://www.nigms.nih.gov/Research/

NIGMS places great emphasis on the support of individual, investigator-initiated grants within its scientific mission areas. Most grants are for research projects (R01), but NIGMS also funds program projects (P01) as well as some research resources. The Institute encourages research in certain scientific areas through requests for applications and program announcements. This website has information for upcoming grants, minority grants as well as training opportunities in medical research in the following disciplines: cell biology, biophysics, genetics, developmental biology, pharmacology, physiology, biological chemistry, bioinformatics, and computational biology.

Proper citation: National Institute of General Medical Sciences: Research Funding (RRID:SCR_003096) Copy   

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http://genome.ucsc.edu/cgi-bin/hgPcr?command=start

Tool that searches a sequence database with a pair of PCR primers, using an indexing strategy for fast performance. When successful, the search returns a sequence output file in fasta format containing all sequence in the database that lie between and include the primer pair. The fasta header describes the region in the database and the primers. The fasta body is capitalized in areas where the primer sequence matches the database sequence and in lower-case elsewhere. Sources and executables to run batch jobs on your own server are available free for academic, personal, and non-profit purposes. Non-exclusive commercial licenses are also available.

Proper citation: In-Silico PCR (RRID:SCR_003089) Copy   

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http://empress.har.mrc.ac.uk

Database of validated Standard Operating Procedures (SOPs) for screens to determine the phenotype of a mouse, developed by the EUMORPHIA consortium. The SOP's cover all of the main body systems including: clinical chemistry, hormonal and metabolic systems, cardiovascular, allergy and infection, renal function, sensory function, neurological and behavioral function, cancer, bone and cartilage, and respiratory function. In addition, there are generic SOPs in histology, necropsy, pathology and gene expression. EMPReSS is a platform of individual tests. These can be performed as individual tests or grouped together in sequences, recommended in the EMPReSS database, to give more information on particular phenotype. Quick List of Current Pipelines: * EUMODIC Pipeline 1 * EUMODIC Pipeline 2 * GMC Pipeline * MGP Pipeline * Additional Tests * EUMODIC Pipeline 3

Proper citation: European Mouse Phenotyping Resource of Standardised Screens (RRID:SCR_003087) Copy   

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http://elm.eu.org

Computational biology resource for investigating candidate functional sites in eukarytic proteins. Functional sites which fit to the description linear motif are currently specified as patterns using Regular Expression rules. To improve the predictive power, context-based rules and logical filters are being developed and applied to reduce the amount of false positives. The current version of the ELM server provides core functionality including filtering by cell compartment, phylogeny, globular domain clash (using the SMART/Pfam databases) and structure. In addition, both the known ELM instances and any positionally conserved matches in sequences similar to ELM instance sequences are identified and displayed (see ELM instance mapper). Although the ELM resource contains a large collection of functional site motifs, the current set of motifs is not exhaustive.

Proper citation: Eukaryotic Linear Motif (RRID:SCR_003085) Copy   

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http://sourceforge.net/projects/gemi/

Automated software tool to design polymerase chain reaction (PCR) primers. It accepts multiple aligned and long sequences with degenerated nucleotides. It can be used for quantitative/real-time PCR, conventional and Sanger sequencing. Gemi accepts DNA and RNA sequences with degenerate nucleotide (non-A/C/G/T bases). The programs are as the following: # The first program is to design PCR primers from multiple sequence alignment. # Program to convert ClustalW format (.aln), Phylip (.phy) and (.gde) formats to Fasta format. # Reverse and/or complement program is to find the reverse and complement counterpart of single or multiple sequences.

Proper citation: Gemi (RRID:SCR_003211) Copy   

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http://sourceforge.net/projects/vtontology/

A controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to the morphology, physiology, or development of vertebrate organisms.

Proper citation: Vertebrate Trait Ontology (RRID:SCR_003214) Copy   

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http://www.popgen.dk/software/index.php/NgsAdmix

A tool for finding admixture proportions from next generation sequencing (NGS) data that is based on genotype likelihoods. It is a multithreaded c/c++ program.

Proper citation: NGSadmix (RRID:SCR_003208) Copy   

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http://www.google.com/sidewiki/intl/en/index.html

THIS RESOURCE IS NO LONGER IN SERVICE, documented July 10, 2017. Sidewiki allows you to publish helpful information about any web page right in your browser, read insights in context from Sidewiki entries added by others, and share Sidewiki entries through Blogger, Facebook, Twitter and Google profiles. The toolbar with Sidewiki is free, installs in seconds and requires Internet Explorer 6+ or Firefox 2+; Windows XP SP2/Vista+. A Google Sidewiki extension is only available for Google Chrome 4.0+

Proper citation: Google Sidewiki (RRID:SCR_003206) Copy   

•   Source: SciCrunch Registry
  

http://www.qgene.org/

A free, open-source, computationally efficient Java program for comparative analyses of QTL mapping data and population simulation that runs on any computer operating system. (entry from Genetic Analysis Software) It is written with a plug-in architecture for ready extensibility. The software accommodates line-cross mating designs consisting of any arbitrary sequence of selfing, backcrossing, intercrossing and haploid-doubling steps that includes map, population, and trait simulators; and is scriptable. Source code is available on request.

Proper citation: QGene (RRID:SCR_003209) Copy   

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http://compgen.bscb.cornell.edu/phast/

A freely available software package for comparative and evolutionary genomics that consists of about half a dozen major programs, plus more than a dozen utilities for manipulating sequence alignments, phylogenetic trees, and genomic annotations. For the most part, PHAST focuses on two kinds of applications: the identification of novel functional elements, including protein-coding exons and evolutionarily conserved sequences; and statistical phylogenetic modeling, including estimation of model parameters, detection of signatures of selection, and reconstruction of ancestral sequences. It consists of over 60,000 lines of C code.

Proper citation: PHAST (RRID:SCR_003204) Copy   

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http://www.csir.res.in

Research and development organization that hosts a knowledgebase in diverse scientific areas. It also hosts a network of national Indian laboratories, outreach centres, and innovation complexes.

Proper citation: Council of Scientific and Industrial Research (RRID:SCR_003203) Copy   

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http://www.hologic.com/

THIS RESOURCE IS NO LONGER IN SERVICE, documented July 7, 2017. Formerly a commercial organization for clinical diagnostics, blood screening, transplant products and research products, it had been acquired by Hologic in 2012.

Proper citation: Gen-Probe (RRID:SCR_003202) Copy   

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https://github.com/hangelwen/miR-PREFeR

An accurate, fast, and easy-to-use plant miRNA prediction software tool using small RNA-Seq data. It utilizes expression patterns of miRNA and follows the criteria for plant microRNA annotation to accurately predict plant miRNAs from one or more small RNA-Seq data samples of the same species.

Proper citation: miR-PREFeR (RRID:SCR_003353) Copy   

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https://github.com/fhcrc/nestly

A Python package to facilitate running tools with nested combinations of parameters and inputs. It provides three components: a module to build nested directory structures corresponding to choices of parameters; the nestrun script to run a given command using each set of parameter choices; the nestagg script to aggregate results of the individual runs into a CSV file, as well as support for more complex aggregation. Also included is a module for easily specifying nested dependencies for the SCons build tool, enabling incremental builds.

Proper citation: Nestly (RRID:SCR_003472) Copy   

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http://cophs.mercer.edu/pharmsci.htm

The mission of the Department of Pharmaceutical Sciences is to make scholarly contributions to the discipline of pharmaceutical sciences and related fields. Education within the department offers a high quality learning environment that includes Ph.D. and Pharm.D./Ph.D. degree programs. Although not required for entry into pharmacy practice, a one-year residency is offered and affords the Pharm.D. graduate an opportunity to develop expertise in clinical pharmacy practice and specialty areas. The graduate program leading to the Ph.D. degree in pharmaceutical sciences is designed for students seeking teaching and research careers in academic institutions, the pharmaceutical industry and other health-related agencies. An interdisciplinary approach prepares graduates to perform independent research, to encourage scholarly development and to acquire teaching skills. Areas of specialization include pharmacology, pharmaceutics, toxicology, and medicinal chemistry. The Doctor of Pharmacy (Pharm.D.)/Doctor of Philosophy (Ph.D.) Degree Program enables highly qualified students to obtain both degrees in a shortened period of time. This Pharm.D./Ph.D. Degree program is designed primarily for students who are strongly motivated toward an academic/ research career in the pharmaceutical sciences. The Program is flexible enough to accommodate individuals of varied educational backgrounds.

Proper citation: Mercer University College of Pharmacy and Health Sciences; Department of Pharmaceutical Sciences (RRID:SCR_003479) Copy   

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http://departments.columbian.gwu.edu/psychology/graduate/cognitiveneuroscience

The Cognitive Neuroscience Program provides graduate students with an intense and focused research experience in the areas of perception, attention, and memory, with emphasis on the neural bases of these capacities. The program utilizes diverse research methods such as patient-based testing, neuro-imaging, animal modeling, and psychophysical scaling, and computational modeling. The goal of the program is to train students for careers in academic and research institutions. At the undergraduate level, the program provides both entry level and advanced courses as well as honor seminars in special topics. The program boasts a high faculty / student ratio, reflecting a strong emphasis on close collaboration between faculty and students on joint research projects. The Washington, DC research environment is outstanding, with the National Institutes of Health, Georgetown University, the University of Maryland, Johns Hopkins University, George Mason University, and other research institutions all close by. GWU's other resources for cognitive neuroscience research include a major medical school, a teaching hospital with world-class Neurology, Neurosurgery and Neuroradiology Departments, and an intensive Neuroscience Program. GWU is located in the heart of Washington, DC, a beautiful city with a wide variety of national museums, historical sites, restaurants, and cultural events. The Cognitive Neuroscience program at GW is designed to train students to become independent scientists who do basic research in an academic setting. Please note that ours is not a clinical neuropsychology program -- we provide no training in diagnosing or treating any brain or neurological disorder.

Proper citation: George Washington University, Cognitive Neuroscience (RRID:SCR_003356) Copy   

•   Source: SciCrunch Registry