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http://sequenceontology.org/

A collaborative ontology for the definition of sequence features used in biological sequence annotation. SO was initially developed by the Gene Ontology Consortium. Contributors to SO include the GMOD community, model organism database groups such as WormBase, FlyBase, Mouse Genome Informatics group, and institutes such as the Sanger Institute and the EBI. Input to SO is welcomed from the sequence annotation community. The OBO revision is available here: http://sourceforge.net/p/song/svn/HEAD/tree/ SO includes different kinds of features which can be located on the sequence. Biological features are those which are defined by their disposition to be involved in a biological process. Biomaterial features are those which are intended for use in an experiment such as aptamer and PCR_product. There are also experimental features which are the result of an experiment. SO also provides a rich set of attributes to describe these features such as polycistronic and maternally imprinted. The Sequence Ontologies use the OBO flat file format specification version 1.2, developed by the Gene Ontology Consortium. The ontology is also available in OWL from Open Biomedical Ontologies. This is updated nightly and may be slightly out of sync with the current obo file. An OWL version of the ontology is also available. The resolvable URI for the current version of SO is http://purl.obolibrary.org/obo/so.owl.

Proper citation: SO (RRID:SCR_004374) Copy   

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http://www.trex.uqam.ca/

A web server dedicated to the reconstruction of phylogenetic trees, reticulation networks and to the inference of horizontal gene transfer (HGT) events.

Proper citation: Tree and reticulogram REConstruction (RRID:SCR_004497) Copy   

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http://bix.ucsd.edu/projects/singlecell/

Software package for short read data from single cells that improves assembly through use of progressively increasing coverage cutoff. Used for single cell Illumina sequences, allows variable coverage datasets to be utilized with assembly of E. coli and S. aureus single cell reads. Assembles single cell genome of uncultivated SAR324 clade of Deltaproteobacteria.

Proper citation: Velvet-SC (RRID:SCR_004377) Copy   

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http://www.bri.ucla.edu/nha/RETICULM.htm

THIS RESOURCE IS NO LONGER IN SERVICE, documented September 6, 2016. RETICULUM is a gateway to Internet resources for history and historians of basic, clinical, and behavioral neuroscience. Links to existing sites are reviewed for salience and accuracy, organized by topic for convenient access, and regularly tested for availability. Comments, questions, and additional resource suggestions and submissions are welcomed. Major categories include: Calendar/Announcements, Professional societies and associations, Internet forums, Placement opportunities, Funding opportunities, Education opportunities, Repositories and collections, Catalogs and indexes, Texts on the Internet, Images on the Internet, Exhibits on the Internet, Periodicals, Commercial resources, Subject guides, Internet introductions, tutorials and tools, Questions-Comments-Suggestions-Submissions, Credits

Proper citation: RETICULUM - Neuroscience History Resources (RRID:SCR_004371) Copy   

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http://rarediseasesnetwork.epi.usf.edu/index.htm

The Rare Diseases Clinical Research Network (RDCRN) was created to facilitate collaboration among experts in many different types of rare diseases. Our goal is to contribute to the research and treatment of rare diseases by working together to identify biomarkers for disease risk, disease severity and activity, and clinical outcome, while also encouraging development of new approaches to diagnosis, prevention, and treatment. The Rare Diseases Clinical Research Network (RDCRN) is made up of 19 distinctive consortia that are working in concert to improve availability of rare disease information, treatment, clinical studies, and general awareness for both patients and the medical community. The RDCRN also aims to provide up-to-date information for patients and to assist in connecting patients with advocacy groups, expert doctors, and clinical research opportunities.

Proper citation: Rare Diseases Clinical Research Network (RRID:SCR_004372) Copy   

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http://www.fnih.org/

A public charity whose mission is to support the NIH in its mission to improve health, by forming and facilitating public-private partnerships for biomedical research and training. Its vision is Building Partnerships for Discovery and Innovation to Improve Health. The FNIH draws together the world''s foremost researchers and resources, pressing the frontier to advance critical discoveries. They are recognized as the number-one medical research charity in the countryleveraging support, and convening high level partnerships, for the greatest impact on the most urgent medical challenges we face today. Grants are awarded as part of a public-private partnership with the National Heart, Lung, and Blood Institute (NHLBI) on behalf of The Heart Truth in support of women''s heart health education and research. Funding for the Community Action Program is provided by the FNIH through donations from individuals and corporations including The Heart Truth partners Belk Department Stores, Diet Coke, and Swarovski. Successful biomedical research relies upon the knowledge, training and dedication of those who conduct it. Bringing multiple disciplines to bear on health challenges requires innovation and collaboration on the part of scientists. Foundation for NIH partnerships operate in a variety of ways and formats to recruit, train, empower and retain their next generation of researchers. From lectures and multi-week courses, to scholarships and awards through fellowships and residential training programs, their programs respond to the needs of scientists at every level and stage in their careers.

Proper citation: Foundation for the National Institutes of Health (RRID:SCR_004493) Copy   

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https://github.com/alyssafrazee/derfinder

R package for differential expression analysis of RNA-seq data.

Proper citation: DER Finder (RRID:SCR_004250) Copy   

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http://www.tcdb.org/

Curated, relational database containing sequence, classification, structural, functional and evolutionary information about transport systems from variety of living organisms based on IUBMB-approved transporter classification (TC) system. Descriptions, TC numbers, and examples of over 600 families of transport proteins are provided. TC system is analogous to Enzyme Commission (EC) system for classification of enzymes, except that it incorporates both functional and phylogenetic information. TCDB users may submit their own sequenced proteins and descriptions for inclusion into database. The software tools used are all freely available for download. These programs are used for analysis of Protein and DNA sequences. Programs require UNIX server to run.

Proper citation: Transporter Classification Database (RRID:SCR_004490) Copy   

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http://www.ncbi.nlm.nih.gov/pmc/

Collection of full text archive of biomedical and life sciences journal literature at U.S. National Institutes of Health National Library of Medicine (NIH/NLM). With PubMed Central, NCBI is taking lead in preserving and maintaining open access to electronic literature. Value of PubMed Central, in addition to its role as an archive, lies in what can be done when data from diverse sources is stored in common format in single repository. All articles in PMC are free (sometimes on a delayed basis). Some journals go beyond free, to Open Access.

Proper citation: PubMed Central (RRID:SCR_004166) Copy   

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http://www.genome.jp/

GenomeNet is a Japanese network of database and computational services for genome research and related research areas in biomedical sciences, operated by the Kyoto University Bioinformatics Center. GenomeNet was established in September 1991 under the Human Genome Program of the then Ministry of Education, Science and Culture (Monbusho). The GenomeNet service has been developed by the Kanehisa Laboratory in Kyoto University as part of the research projects. GenomeNet is operated using the Supercomputer System of the Institute for Chemical Research, Kyoto University. LinkDB is supported by the National Bioscience Database Center of the Japan Science and Technology Agency.

Proper citation: GenomeNet (RRID:SCR_004165) Copy   

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http://pubchem.ncbi.nlm.nih.gov/

Collection of information about chemical structures and biological properties of small molecules and siRNA reagents hosted by the National Center for Biotechnology Information (NCBI).

Proper citation: PubChem (RRID:SCR_004284) Copy   

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http://sourceforge.net/projects/insertionmapper/

A pipeline tool for the identification of targeted sequences from multidimensional high throughput sequencing data. It consists of four independently working modules: Data Preprocessing, Database Modeling, Dimension Deconvolution and Element Mapping. This pipeline tool is applicable to scenarios requiring analysis of the tremendous output of short reads produced in NGS sequencing experiments of targeted genome sequences.

Proper citation: InsertionMapper (RRID:SCR_004163) Copy   

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http://www.nitrc.org/ir/

Data repository for neuroimaging data in DlCOM and NIFTI formats. It allows users to search for and freely download publicly available data sets relating to normal subjects and those with diagnoses such as: schizophrenia, ADHD, autism, and Parkinson's disease.XNAT-based image registry that supports both NIfTI and DICOM images to promote re-use and integration of NIH funded data.

Proper citation: NITRC-IR (RRID:SCR_004162) Copy   

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http://www.neuromatic.thinkrandom.com/

NeuroMatic is a collection of Igor Pro functions for analyzing electrophysiological data. By allowing users to organize their data into Sets and Groups, NeuroMatic makes it relatively easy to compute transformations and statistical analyses on their data, including scaling, alignment averaging, baseline subtraction, spike detection, stationarity analysis, rise-time computations, etc. Being open source and modular designed, NeuroMatic also allows users to develop their own analysis functions that can be easily incorporated into NeuroMatic's framework. Note, if you have reached this page in search of a freeware tool for neuronal reconstructions, you are more likely to be interested in Neuromantic, a software package that sounds like NeuroMatic, but is not quite the same. Features of NeuroMatic Include * Sorting, Scaling, Averaging, Interpolation * Max / Min / Mean / Level / Rise Time / FWHM / Slope Measurements * Stability / Stationarity Analysis * Event Detection * Waveform Template Matching * Spike Raster Plots * Interspike-Interval and Peri-Stimulus Time (PST) Histograms * Compact Easy-to-Use Interface * Modular design as a basis for your own procedures * Extra space for your own buttons and controls * Import functions for Axograph and Pclamp data * Automatic macro generation for batch processing Supporting Agencies: MRC, Wellcome Trust Spike, Event, Fit, NClamp, Acquisition, spike train, EPSP, IPSP, IPSC, EPSC

Proper citation: NeuroMatic (RRID:SCR_004186) Copy   

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http://www.fmi.ch/

The Friedrich Miescher Institute is devoted to fundamental biomedical research aimed at understanding the basic molecular mechanisms of health and disease. We communicate and patent our findings to enable their translation into medical application. The FMI focuses on the fields of Epigenetics, Signaling & Cancer, and Neurobiology. In these fields, the FMI has gained international recognition as a center of excellence in innovative biomedical research. Training young scientists The Friedrich Miescher Institute contributes to the training of graduate students and postdoctoral fellows. Through its PhD program, which was established as early as 1970, the FMI attracts top international students. The FMI is affiliated with the University of Basel, where most of the graduate students are enrolled and where it contributes to the teaching program. Many FMI alumni have gone on to pursue successful careers in Novartis, in other pharmaceutical companies, or in academic research. Exciting environment for academic and applied research Staff at FMI benefit from a unique scientific environment, allowing researchers, specialists and students to pursue questions that yield new scientific insights. As part of the Novartis Research Foundation, the FMI receives strong core support from the foundation. Funding is supplemented by competitive fellowships and awards from national and international funding agencies. This provides an optimal environment for both academic and applied biomedical research.

Proper citation: Friedrich Miescher Institute (RRID:SCR_004179) Copy   

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http://annotationframework.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023. The DOMEO (Document Metadata Organizer) Annotation Tool, is an extensible web component enabling users to visually and efficiently create and share ontology-based stand-off annotation metadata on HTML or XML document targets - and soon images - , using the Annotation Ontology (AO) RDF model. The tool supports manual, fully automated, and semi-automated annotation with complete provenance records, as well as personal or community annotation with access authorization and control. DOMEO is just one of the components of a bigger architecture - The Annotation Framework - that uses Annotation Ontology (AO) as communication mechanism within the platform and with the external world. Acknowledgements Special thanks to Marco Ocana for his valuable contribution in bootstrapping the DOMEO project.

Proper citation: DOMEO (RRID:SCR_004170) Copy   

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http://genome.gsc.riken.jp/osc/english/dataresource/

A program to eliminate artifactual reads from next-generation sequencing data sets.

Proper citation: TagDust (RRID:SCR_004175) Copy   

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http://www.cfcsyndrome.org/index.shtml

CFC International is a volunteer, not-for profit, self-help support group for persons and families dealing with Cardio-Facio-Cutaneous Syndrome. Incorporated in 1999 in the state of New York, its membership has grown from 21 families in mainly the USA to now include persons from all around the world. Our mission is to strive to help each other cope with the challenges of raising a child with a rare and often medically involved disorder. We act as a clearinghouse of information on all aspects of CFC Syndrome. We publish a quarterly newsletter, produce a brochure and CFC Parent''''s Guide, private address book, host a private family computer list serve and also host a website. We host International family conferences and clinics open to families from all over the globe. Our goal is to educate the general public, the medical profession, and government agencies by disseminating information on CFC Syndrome. We work to facilitate research on this very rare syndrome. We have a medical/scientific advisory board consisting of doctors from different regions of the world who have a committed interest in our CFC children. We maintain the most extensive registry for CFC Syndrome patients in the world. The Registry provides resources for the study of CFC Syndrome. It maintains centralized information records on CFC Syndrome cases from around the world. Confidentiality of personal information regarding incidence, genetics, clinical course, and prognosis is provided to professionals and families. The Registry also serves to improve communication of ideas among interested researchers, and to assure rapid distribution of any new information that may benefit patients or their families. As part of this medical registry we are founding members of the Genetic Alliance BioBank. The BioBank contains the largest collection of DNA and tissue samples from CFC patients and their parents.

Proper citation: CFC International (RRID:SCR_004174) Copy   

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http://theorylab.org/

The primary aim of the KLI Theory Lab is to highlight interconnections between topics of problems of research on evolution and cognition that look theoretically or methodologically promising. Quite often such correlations remain unrecognized because of the disciplinary closure that characterizes the organization of the scientific enterprise. * Introductory Resources: Introductory texts to various relevant disciplines, provided by the Konrad Lorenz Institute include: ** Introduction to Artificial Intelligence ** Introduction to Artificial Life ** Introduction to Cognitive Science ** Introduction to Cultural Evolution ** Introduction to Developmental Biology ** Introduction to Epistemology & Philosophy of Science ** Introduction to Ethology & Sociobiology ** Introduction to Evolutionary Biology ** Introduction to Evolutionary Epistemology ** Introduction to Genetic Epistemology ** Introduction to History and Social Sciences ** Introduction to Normative Issues ** Introduction to Philosophy of Biology ** Introduction to Philosophy of Mind ** Introduction to Theoretical Biology * Reference Database: The KLI Theory Lab contains a vast collection of research papers that have been selected based on their significance and quality. ** Search references: The search page allows you to search for references and to narrow down your search based on keywords. Results are ordered by relevance. ** Browse references: All references in the database, ordered by date of publication.

Proper citation: KLI Theory Lab (RRID:SCR_004290) Copy   

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http://cran.r-project.org/web/packages/kdetrees/

R package using a non-parametric method for estimating distributions of phylogenetic trees, with the goal of identifying trees that are significantly different from the rest of the trees in the sample.

Proper citation: Kdetrees (RRID:SCR_004522) Copy   

•   Source: SciCrunch Registry