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https://docs.python.org/2/library/random.html

This module implements pseudo-random number generators for various distributions. For integers, uniform selection from a range. For sequences, uniform selection of a random element, a function to generate a random permutation of a list in-place, and a function for random sampling without replacement. On the real line, there are functions to compute uniform, normal (Gaussian), lognormal, negative exponential, gamma, and beta distributions. For generating distributions of angles, the von Mises distribution is available. Sponsors: This resource is supported by ASTi logo Advanced Simulation Technology Inc. (ASTi); Array BioPharma Inc.; BizRate.com; Canonical Ltd.; CCP Games; cPacket Networks; EarnMyDegree.com; Enthought Inc.; Exoweb Ltd.; Google; HitMeister Inc.; IronPort Systems; KNMP; Lucasfilm; Madison Tyler LLC.; Merfin, LLC.; Microsoft; OpenEye Scientific Software; Opsware, Inc.; O''Reilly & Associates, Inc.; PropertySold.ca; Rogue Wave; SEO Moves; Strakt Holdings, Inc.; Sun Microsystems; Tabblo; ZeOmega, LLC., and Zope Corporation.

Proper citation: Generate Pseudo-Random Numbers (RRID:SCR_006535) Copy   

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http://archive.igbmc.fr/recherche/Prog_FGC/Eq_HGron/Bioinfotools/NGS/website/index.php

Computational-based software that infers quality indicators from the distribution of sequenced reads associated to a particular NGS profile. Such information is then used for comparative purposes and for defining strategies to improve the quality of sample-derived datasets.

Proper citation: NGS-QC Generator (RRID:SCR_006536) Copy   

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http://ctdbase.org/

A public database that enhances understanding of the effects of environmental chemicals on human health. Integrated GO data and a GO browser add functionality to CTD by allowing users to understand biological functions, processes and cellular locations that are the targets of chemical exposures. CTD includes curated data describing cross-species chemical–gene/protein interactions, chemical–disease and gene–disease associations to illuminate molecular mechanisms underlying variable susceptibility and environmentally influenced diseases. These data will also provide insights into complex chemical–gene and protein interaction networks.

Proper citation: Comparative Toxicogenomics Database (CTD) (RRID:SCR_006530) Copy   

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https://bitbucket.org/wanding/duprecover/overview

Software that facilitates accurate estimation for sampling-induced read duplication in deep sequencing experiments.

Proper citation: DupRecover (RRID:SCR_006410) Copy   

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http://davinci.crg.es/deafness/

Database and data set of known mutations in connexins related to deafness with associated information including published work and classification scheme. Users may submit new mutations. A large number of subjects are affected by hearing impairment. In developed countries deafness has an important genetic origin and at least 60% of the cases are inherited. The pattern of inheritance can be dominant, recessive, X-linked and mitochondrial. Many genes are involved in the different types of deafness (syndromic and non-syndromic). Non-syndromic hereditary deafness is mainly (80%) due to recessive genes (or mutations). It is believed that more than one hundred genes could be involved in hearing impairment. Several of these genes have been identified recently by positional cloning or positional candidate gene approaches. Despite the fact that more than 20 loci have been described for non-syndromic autosomal recessive deafness (DFNB), a single locus, DFNB1, accounts for a high proportion of the cases, with variability depending on the population. The gene involved in this type of deafness is GJB2, which encodes the gap junction protein connexin 26(Cx26). NEW Recent data indicates that DFNB1 can also be due to a deletion of 342Kb involving GJB6, a gene that is very close to GJB2. This deletion has been reported to cause deafness both in the homozygous status and in heterozygosity with a GJB2 point mutation in trans (see big deletions affecting connexin genes...). Connexins are transmembrane proteins that form channels allowing rapid transport of ions or small molecules between cells. There are two types of connexins, alpha and beta, named GJA or GJB followed by a number. Connexins are expressed in many different tissues. Other connexin genes are also involved in deafness. These are GJB1 (Cx32), which is also responsible for X-linked Charcot-Marie-Tooth disease type I; GJB3 (Cx31), involved in both deafness or a skin disease, erythrokeratodermia variabilis, depending on the location of the mutation; GJB6 (Cx30), which has been related to a dominant type of deafness in an Italian family and NEW GJA1 (Cx43), which has recently been shown to be involved in recessive deafness.

Proper citation: Connexin-deafness (RRID:SCR_006531) Copy   

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http://bioinf.wehi.edu.au/socrates/

Software for detecting genomic rearrangements in tumors that utilizes only split-read data. It features single nucleotide resolution, high sensitivity, and high specificity in simulated data. It takes advantage of parallelism for efficient use of resources.

Proper citation: Socrates (RRID:SCR_006411) Copy   

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https://www.phenxtoolkit.org/

Set of measures intended for use in large-scale genomic studies. Facilitate replication and validation across studies. Includes links to standards and resources in effort to facilitate data harmonization to legacy data. Measurement protocols that address wide range of research domains. Information about each protocol to ensure consistent data collection.Collections of protocols that add depth to Toolkit in specific areas.Tools to help investigators implement measurement protocols.

Proper citation: Phenotypes and eXposures Toolkit (RRID:SCR_006532) Copy   

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http://www.roslin.ed.ac.uk/

World class research center that undertakes top-class basic and translational science to tackle some of the most pressing issues in animal health and welfare, their implications for human health and for the role of animals in the food chain. Roslin provides holistic solutions to global challenges in human and veterinary medicine and the livestock industry. Its mission is to gain fundamental understanding of genetic, cellular, organ and systems bioscience underpinning common mechanisms of animal development and pathology, and to drive this into prevention and treatment of important veterinary diseases and develop sustainable farm animal production systems. The Roslin Institute aims to enhance the lives of animals and humans through world class research in animal biology. The principal objectives are to: * Enhance animal health and welfare through knowledge of genetic factors affecting resistance to disease. * Enhance sustainability and productivity of livestock systems and food supply chains through understanding of reproductive and developmental biology. * Enhance food safety by understanding interactions between disease causing organisms and animals. * Enhance human health through an understanding of basic mechanisms of health and disease and comparative biology of animal species. * Identify of new and emerging zoonoses and understand how pathogens might cross from animals to humans. * Enhance quality of life for animals by studying the mechanisms and behaviors associated with optimizing their environment and life experiences.

Proper citation: Roslin Institute (RRID:SCR_006533) Copy   

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http://nkdep.nih.gov/

Educational resource to increase awareness of kidney disease and its risk factors, improve early detection of chronic kidney disease (CKD), reduce the burden of CKD, facilitate identification of patients at greatest risk for progression to kidney failure, stress the importance of testing those at risk, promote evidence-based interventions to slow progression of CKD, and support the coordination of Federal responses to CKD. Target audiences include individuals at risk, particularly those with diabetes, high blood pressure, and a family history of kidney disease, and primary care providers.

Proper citation: National Kidney Disease Education Program (RRID:SCR_006527) Copy   

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http://bioinformatics.oxfordjournals.org/content/early/2014/01/02/bioinformatics.btt759.abstract?sid=e62f3c2b-26dc-428b-ba24-99e92a277d77

Statistical software to estimate tumor purity, ploidy and absolute copy numbers from next generation sequencing data.

Proper citation: AbsCN-seq (RRID:SCR_006409) Copy   

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http://vinovia.ncl.ac.uk/emagewebapp/pages/eadhb_home.jsf

Database of a set of standard 3D virtual models at different stages of development from Carnegie Stages (CS) 12-23 (approximately 26-56 days post conception) in which various anatomical regions have been defined with a set of anatomical terms at various stages of development (known as an ontology). Experimental data is captured and converted to digital format and then mapped to the appropriate 3D model. The ontology is used to define sites of gene expression using a set of standard descriptions and to link the expression data to an ''''anatomical tree''''. Human data from stages CS12 to CS23 can be submitted to the HUDSEN Gene Expression Database. The anatomy ontology currently being used is based on the Edinburgh Human Developmental Anatomy Database which encompasses all developing structures from CS1 to CS20 but is not detailed for developing brain structures. The ontology is being extended and refined (by Prof Luis Puelles, University of Murcia, Spain) and will be incorporated into the HUDSEN database as it is developed. Expression data is annotated using two methods to denote sites of expression in the embryo: spatial annotation and text annotation. Additionally, many aspects of the detection reagent and specimen are also annotated during this process (assignment of IDs, nucleotide sequences for probes etc). There are currently two main ways to search HUDSEN - using a gene/protein name or a named anatomical structure as the query term. The entire contents of the database can be browsed using the data browser. Results may be saved. The data in HUDSEN is generated from both from researchers within the HUDSEN project, and from the wider scientific community. The HUDSEN human gene expression spatial database is a collaboration between the Institute of Human Genetics in Newcastle, UK, and the MRC Human Genetics Unit in Edinburgh, UK, and was developed as part of the Electronic Atlas of the Developing Human Brain (EADHB) project (funded by the NIH Human Brain Project). The database is based on the Edinburgh Mouse Atlas gene expression database (EMAGE), and is designed to be an openly available resource to the research community holding gene expression patterns during early human development.

Proper citation: HUDSEN Human Gene Expression Spatial Database (RRID:SCR_006325) Copy   

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http://www.informatics.jax.org/searches/AMA_form.shtml

Ontology that organizes anatomical structures for the adult mouse (Theiler stage 28) spatially and functionally, using ''is a'' and ''part of'' relationships. The ontology is used to describe expression data for the adult mouse and phenotype data pertinent to anatomy in standardized ways. The browser can be used to view anatomical terms and their relationships in a hierarchical display.

Proper citation: Adult Mouse Anatomy Ontology (RRID:SCR_006568) Copy   

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http://www.neuroinf.jp/

The Japan Node of the INCF coordinates neuroinformatics activities within Japan and represents Japanese efforts in INCF. This site provides information about Japanese neuroinformatics platforms (NI Platforms) and the techniques and tools available from the International Neuroinformatics Coordinating Facility (INCF). The Neuroinformatics Japan Center (NIJC) will also supply techniques and tools developed at RIKEN BSI and at other research groups in Japan. INCF expects each national node to: 1. Actively formulate and implement the INCF Work Programs, 2. Coordinate and facilitate local neuroinformatics research activities at the national level, 3. Encourage neuroinformatics data sharing that conforms with INCF standards, and 4. Promote neuroinformatics development that supports the goals of INCF. The Neuroinformatics Japan Center (NIJC) represents the Japan Node. Together with the Japan Node Committee and the Platform Subcommittees, we promote domestic activities of neuroinformatics. Platform Subcommittee members collaborate to develop databases that are available for use on the website. Standing at the intersection of neuroscience and information science, the field of neuroinformatics develops the tools to house, share and analyze neuroscientific data, and to create computational models of brain. NIJC supports researchers developing and maintaining neuroscience databases, provides a portal for these databases and Neuroinformatics, and is designing the infrastructure for Neuroinformatics. It is also developing database technologies, and facilitates cooperation and distribution of the information stored in those databases. The activities of the Japan Node * Shaping domestic neuroinformatics research and directions (Japan Node Committee) * Advising on Intellectual Property Rights and protecting experimental subjects (Japan Node Committee) * Developing and publishing brain science databases (Platform Subcommittee) * Coordinating database management (Platform Subcommittee) * Disseminating neuroinformatics information via the web portal * Developing the infrastructure for brain science information and neuroinformatics * Supporting the development and diffusion of neuroinformatics technology

Proper citation: INCF Japan Node (RRID:SCR_006569) Copy   

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http://www.endo-society.org/

Founded in 1916, The Endocrine Society is the world''s oldest, largest, and most active organization devoted to research on hormones and the clinical practice of endocrinology. The Society works to foster a greater understanding of endocrinology amongst the general public and practitioners of complementary medical disciplines and to promote the interests of all endocrinologists at the national scientific research and health policy levels of government. The Endocrine Society publishes four world-renowned journals and a monthly news magazine, holds scientific conferences, provides educational programs for physicians, issues clinical practice guidelines, promotes careers in endocrinology, and advocates for appropriate funding of scientific research in endocrinology and public policies that support the practice of clinical endocrinology. The Hormone Health Network, the Society''s public education affiliate, is a leading source of hormone-related health information for the public, physicians, allied health professionals and the media. The Endocrine Society is an international body with more than 15,000 members from over 100 countries. The Society''s diverse membership represents medicine, molecular and cellular biology, biochemistry, physiology, genetics, immunology, education, industry and allied health fields. Members of The Endocrine Society represent the full range of disciplines associated with endocrinologists: clinicians, researchers, educators, fellows and students, industry professionals and health professionals who are involved in the field of endocrinology. These professionals are dedicated to the research and treatment of the full range of endocrine disorders: diabetes, reproduction, infertility, osteoporosis, thyroid disease, obesity/lipids, growth hormone, pituitary tumors, and adrenal insufficiency.

Proper citation: Endocrine Society (RRID:SCR_006449) Copy   

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http://www.ontobee.org/

Web-based linked data server and browser specifically designed for ontology terms, it supports ontology visualization, query, and development. Ontobee provides a web interface for displaying the details and hierarchy of a specific ontology term. Meanwhile, Ontobee provides a RDF source code for the particular web page, which supports remote query of the ontology term and the Semantic Web. Ontobee provides an efficient and publicly available method to promote ontology sharing, interoperability, and data integration.

Proper citation: Ontobee (RRID:SCR_006321) Copy   

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http://rgd.mcw.edu

Database for genetic, genomic, phenotype, and disease data generated from rat research. Centralized database that collects, manages, and distributes data generated from rat genetic and genomic research and makes these data available to scientific community. Curation of mapped positions for quantitative trait loci, known mutations and other phenotypic data is provided. Facilitates investigators research efforts by providing tools to search, mine, and analyze this data. Strain reports include description of strain origin, disease, phenotype, genetics, immunology, behavior with links to related genes, QTLs, sub-strains, and strain sources.

Proper citation: Rat Genome Database (RGD) (RRID:SCR_006444) Copy   

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http://www.gigasciencejournal.com/

An online open-access open-data journal, publishing ''big-data'' studies from the entire spectrum of life and biomedical sciences whose publication format links standard manuscript publication with its affiliated database, GigaDB, that hosts all associated data, provides data analysis tools, cloud-computing resources, and a DOI assignment to every dataset. GigaScience covers not just ''omic'' type data and the fields of high-throughput biology currently serviced by large public repositories, but also the growing range of more difficult-to-access data, such as imaging, neuroscience, ecology, cohort data, systems biology and other new types of large-scale sharable data. Supporting the open-data movement, they require that all supporting data and source code be publicly available in a suitable public repository and/or under a public domain CC0 license in the BGI GigaScience database. Using the BGI cloud as a test environment, they also consider open-source software tools / methods for the analysis or handling of large-scale data. When submitting a manuscript, please contact them if you have datasets or cloud applications you would like them to host. To maximize data usability submitters are encouraged to follow best practice for metadata reporting and are given the opportunity to submit in ISA-Tab format.

Proper citation: GigaScience (RRID:SCR_006565) Copy   

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http://www.hudsen.org/

Forum for researchers in human developmental biology and related fields to meet and establish links.

Proper citation: HUDSEN (RRID:SCR_006324) Copy   

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http://wiki.chasmsoftware.org/index.php/Main_Page

CHASM is a method that predicts the functional significance of somatic missense mutations observed in the genomes of cancer cells, allowing mutations to be prioritized in subsequent functional studies, based on the probability that they give the cells a selective survival advantage. SNV-Box is a database of pre-computed features of all possible amino acid substitutions at every position of the annotated human exome. Users can rapidly retrieve features for a given protein amino acid substitution for use in machine learning.

Proper citation: CHASM/SNV-Box (RRID:SCR_006445) Copy   

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http://www.emedicinehealth.com/script/main/hp.asp

eMedicineHealth.com is a consumer health information site that was launched in May 2003. The site contains over 900 health and medical articles written by physicians for patients and consumers. If you are interested in authoring one or more articles, or if you are interested in becoming a medical editor for eMedicineHealth, please see our Medical Writer and Medical Editor submission form for more information. You may search for information or use the Topics from A-Z option. Additionally, Slideshow pictures, Image gallery, Medications, Quizzes, and Medical Dictionary sections are available. eMedicineHealth.com''s main office is in San Clemente, California, and the corporate office is in New York, New York.

Proper citation: emedicinehealth:experts for everyday emergencies (RRID:SCR_006561) Copy   

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