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http://www.nitrc.org/projects/multimpute/

A software toolkit that performs multiple imputation for group level, single sample t-tests. Whole brain group level statistic maps from fMRI rarely cover the entire brain as a result of missing data. Missingness between subjects in fMRI datasets can result from susceptibility artifacts, bounding box (acquisition parameters), and small differences in post-normalized morphology. The toolkit consists of several interactive command line scripts that guide the user to map the spatial distribution of missing data across contrast images, calculate spatial neighborhood averages that help impute values, perform conventional and multiple imputed t-statistics, save the results to brain maps, and create result tables. The toolkit contains an instruction manual (pdf), two Matlab scripts and one R-Statistics script, which depend on functions defined in the popular SPM toolbox and functions defined in the MICE package for (R).

Proper citation: Group Level Imputation of Statistic Maps (RRID:SCR_002397) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/CBBresearch/Schaffer/pedhunter.html

Software package that facilitates creation and verification of pedigrees within large genealogies. The pedigrees are produced as files in LINKAGE format ready for linkage analysis and for drawing with a variety of drawing programs, such as PEDDRAW and cranefoot.

Proper citation: PEDHUNTER (RRID:SCR_002031) Copy   

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http://www.sph.umich.edu/csg/abecasis/LAMP/

Software for linkage and association modeling in pedigrees that uses a maximum likelihood model to extract information on genetic linkage and association from samples of unrelated individuals, sib pairs, trios and larger pedigrees (Li et al, 2005; Li et al, 2006). It provides estimates of genetic model parameters and powerful tests of association in settings where population stratification is not a concern.

Proper citation: LAMP (RRID:SCR_001740) Copy   

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http://www.utsouthwestern.edu/labs/acute-liver/

Clinical research network for gathering prospective data and bio-samples on acute liver failure in adults since 1998. Clinical histories and laboratory and outcome data are available. Sample types include serum, plasma, urine, DNA, and liver tissue.

Proper citation: Acute Liver Failure Study Group (RRID:SCR_001463) Copy   

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http://www.broadinstitute.org/software/syzygy/

A targeted sequencing post processing analysis software tool that allows: 1. SNP and indel detection; 2. Allele frequency estimation; 3. Single-marker association test; 4. Group-wise marker test association; 5. Experimental QC summary (%dbSNP, Ts/Tv, Ns/S); 6. Power to detect variant. (entry from Genetic Analysis Software)

Proper citation: SYZYGY (RRID:SCR_002157) Copy   

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https://abctb.org.au/abctbNew2/default.aspx

A tissue bank which houses and supplies cancerous tissue for use by the research community. Along with tissue, the bank collects clinical history, lifestyle factors, breast pathology, treatment information, and follow up information.

Proper citation: Australia Breast Cancer Tissue Bank (RRID:SCR_000926) Copy   

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http://www.ncbcs.org/biositemaps/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 27,2023. Biositemaps represent a mechanism for computational biologists and bio-informaticians to openly broadcast and retrieve meta-data about biomedical data, tools and services (i.e., biomedical resources) over the Internet. All Institutions with an interest in biomedical research can publish a biositemap.rdf file on their Internet site. The technology, developed by the Biositemaps Working Group of the NIH Roadmap National Centers of Biomedical Computing (NCBC), addresses (i) locating, (ii) querying, (iii) composing or combining, and (iv) mining biomedical resources. Each site which intends to contribute to the inventory instantiates a file on its Internet site biositemap.rdf which conforms to a defined RDF schema and uses concepts from the Biomedical Resource Ontology to describe the resources. Each biositemap.rdf file is simply a list of controlled metadata about resources (software tools, databases, material resources) that your organization uses or believes are important to biomedical research. The key enabling technologies are the Information Model (IM) which is the list of metadata fields about each resource (resource_name, description, contact_person, resource_type,...) and the Biomedical Resource Ontology (BRO) which is a controlled terminology for the resource_typeand which is used to improve the sensitivity and specificity of web searches. Biositemaps blend the features of Sitemaps (enabling efficient web-content exploration) and RSS Feeds (a mechanism for wide and effective news dissemination). As a hybrid between Sitemaps and RSS feeds, the Biositemap infrastructure facilitates a decentralized, portable, extensible and computationally tractable generation and consumption of meta-data about existent, revised and new resources for biomedical computation. Web browsers, crawlers and robots can discover, accumulate, process, integrate and deliver Biositemaps content to (human or machine) users in a variety of graphical, tabular, computational formats. Biositemaps content allows such web browsers to pool resource-associated metadata from disparate and diverse sites and present it to the user in an integrated fashion. The Biositemaps protocol provides clues, information and directives for all Biositemap web harvesters that point to the existence and content of such biomedical resources at different sites.

Proper citation: Biositemaps (RRID:SCR_001976) Copy   

•   Source: SciCrunch Registry

https://wfcc.info/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Collects, authenticates, maintains and distributes cultures of microorganisms and cultured cells. Its aim is to promote and support the establishment of culture collections and related services, to provide liaison and set up an information network between the collections and their users, to organize workshops and conferences, publications and newsletters and work to ensure the long term perpetuation of important collections. The WFCC (through the activities of Professor Skerman, University of Queensland, Australia, and his colleagues in the 1960's) pioneered the development of an international database on culture resources worldwide. The result is the WFCC World Data Center for Microorganisms (WDCM). This data resource is now maintained at National Institute of Genetics (NIG), Japan and has records of nearly 476 culture collections from 62 countries. The records contain data on the organization, management, services and scientific interests of the collections. Each of these records is linked to a second record containing the list of species held. The WDCM database forms an important information resource for all microbiological activity and also acts as a focus for data activities among WFCC members.

Proper citation: World Federation for Culture Collections (RRID:SCR_001974) Copy   

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http://cgsc.biology.yale.edu/index.php

The CGSC Collection contains only non-pathogenic BSL-1 laboratory strains, primarily genetic derivatives of Escherichia coli K-12, the laboratory strain widely used in genetic and molecular studies, but a few B strains. The CGSC Database of E. coli genetic information includes genotypes and reference information for the strains in the CGSC collection, the names, synonyms, properties, and map position for genes, gene product information, and information on specific mutations and references to primary literature. The public version of the database includes this information and can be queried directly via this CGSC DB WebServer. The collection includes cultures of wild-type contributed from a number of laboratories and a few thousand derivatives carrying one or up to 29 mutations from among 3500 mutations in (or included in deletions spanning) more than 1300 different loci. Some combinations were constructed particularly for mapping purposes and are still used for teaching and for rapid localization, some for manifestation of a particular phenotype, some strains for transferring a particular region or for complementation analysis. Some plasmids, e.g., the Clarke and Carbon collection, F-primes, a number of toolkit plasmids, and a few classic plasmids are included, but it is not a comprehensive collection of plasmids. Additionally, we have recently acquired most of the strains from the Keio Collection of systematic individual gene knockout (deletion/kan insertion) strains.

Proper citation: CGSC (RRID:SCR_002303) Copy   

•   Source: SciCrunch Registry

http://www.kbarlivestock.com/

A business that supplies livestock organisms and equipment to biomedical researchers and teachers. Examples of services include livestock such as sheep, goats, swine, and calves; materials such as blood, isolated tissue, feed, hay, equipment; and timed pregnancies and pre-delivery laboratory tests.

Proper citation: K Bar Livestock (RRID:SCR_000924) Copy   

•   Source: SciCrunch Registry

http://mayoresearch.mayo.edu/mayo/research/schaid_lab/software.cfm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. Software application that calculates an exact stratified test for HWE for diallelic markers, such as single nucleotide polymorphisms (SNPs), and an exact test for homogeneity of Hardy Weinberg disequilbrium. In addition, exact tests for HWE are calculated for each stratum. (entry from Genetic Analysis Software)

Proper citation: HWESTRATA (RRID:SCR_001097) Copy   

•   Source: SciCrunch Registry

http://www.biocytex.com/

A French biotech company that specializes in the development of standardized flow cytometry kits in the field of haemostasis. It became part of the Stago group in 1994.

Proper citation: BioCytex (RRID:SCR_001135) Copy   

•   Source: SciCrunch Registry

https://www.origene.com/

Commercial supplier of biomaterials such as antibodies, antigens, lysates, and various assay kits.

Proper citation: Acris Antibodies (RRID:SCR_001095) Copy   

•   Source: SciCrunch Registry

http://jena.sourceforge.net/

Java framework for building Semantic Web applications, it provides a collection of tools and Java libraries to help you to develop semantic web and linked-data apps, tools and servers. It provides extensive Java libraries for helping developers develop code that handles RDF, RDFS, RDFa, OWL and SPARQL in line with published W3C recommendations. Jena includes a rule-based inference engine to perform reasoning based on OWL and RDFS ontologies, and a variety of storage strategies to store RDF triples in memory or on disk. The Jena Framework includes: * an API for reading, processing and writing RDF data in XML, N-triples and Turtle formats; * an ontology API for handling OWL and RDFS ontologies; * a rule-based inference engine for reasoning with RDF and OWL data sources; * stores to allow large numbers of RDF triples to be efficiently stored on disk; * a query engine compliant with the latest SPARQL specification * servers to allow RDF data to be published to other applications using a variety of protocols, including SPARQL In April 2012, Jena graduated from the Apache incubator process and was approved as a top-level Apache project.

Proper citation: JENA: A Semantic Web Framework for Java (RRID:SCR_001766) Copy   

•   Source: SciCrunch Registry

http://www.bios.unc.edu/~lin/software/GAS2/

Software application for evaluating Statistical Significance in Two-Stage Genomewide Association Studies (entry from Genetic Analysis Software)

Proper citation: GAS2 (RRID:SCR_001126) Copy   

•   Source: SciCrunch Registry

http://web.bioinformatics.ic.ac.uk/eqtlexplorer/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. An eQTL visualization tool that allows users to mine and understand data from a repository of genetical genomics experiments (entry from Genetic Analysis Software)

Proper citation: EQTL EXPLORER (RRID:SCR_001123) Copy   

•   Source: SciCrunch Registry

http://www.idoimaging.com/program/218

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. DOCUMENTED NOVEMBER 17, 2016: This program was removed on 03/18/15 and is not being monitored.A software visualization package for the symbolic display of functional neuroimaging datasets in an anatomical context. Written in IDL.

Proper citation: Corner Cube Environment (RRID:SCR_001080) Copy   

•   Source: SciCrunch Registry

http://ngsutils.org/

A suite of software tools for analyzing and manipulating next-generation sequencing datasets, such as FASTQ, BED and BAM format files. These tools provide a stable and modular platform for data management and analysis.

Proper citation: NGSUtils (RRID:SCR_001236) Copy   

•   Source: SciCrunch Registry

http://people.virginia.edu/~wc9c/TDTPC/Download.htm

Software program to compute the statistical power of the Transmission/Disequilibrium Test (TDT) analytically, based on the most accurate asymptotic algorithms up to date, and is applicable in very general situations, where different parental disease status, multiple children, mixed family type and recombination events are considered. Routine algorithms for Monte Carlo simulations with significant improvements are also implemented in this program. (entry from Genetic Analysis Software)

Proper citation: TDT-PC (RRID:SCR_001116) Copy   

•   Source: SciCrunch Registry

http://www.biobank.unisi.it/Elencorett.asp

Data and biospecimen from Rett Syndrome patients shared with the scientific community with the ability to visualize the list of available samples and select those with specific clinical and molecular features. It also contains information on biospecimen samples from x-linked retardation, microdeletion, duplication syndromes, autosomal MR, and retinoblastoma. The bank is active since 1998 and it is located in the Medical Genetics Unit, at the University Hospital of Siena. The bank is divided in three distinct sections: # Rett Syndrome. This section contains samples from patients affected by Rett syndrome, a neurodegenerative disease affecting almost exclusively girls with an estimated frequency of 1:10000-15000 live born. By accessing the section users can see a list of all patients available with their phenotype, the specific MECP2 or CDKL5 mutation if known and the kind of biological samples available for each patient. The availability of this large panel of patients is potentially important for the clarification of the molecular bases of Rett syndrome. In fact, a 20-30 of Rett cases do not have MECP2 or CDKL5 mutations. These patients might bear intronic/promoter MECP2 or CDKL5 mutations or they might have alterations in one or more genes different from MECP2 or CDKL5, as suggested by the identification of various chromosomal rearrangements. To confirm a causative role of these rearrangements, and to identify the relevant gene/s, it is important to collect a great number of patients in which to search for overlapping rearrangements or point mutations in candidate genes. # X-Linked Mental Retardation. This section contains samples collected by the centers belonging to the Italian network on X-linked mental retardation, which includes the laboratory of bank curators (for specific information on the network goals and organization, go to the section page). Mental retardation (MR) is the most frequent cause of serious handicap in humans with an estimated prevalence of 0,3-0,5 for moderate to severe MR (IQ<50) which increases to 1-1,5 when mild MR (IQ 50-70) is included. It is calculated that about 20-25 of mentally retarded males have a mutation in a gene on the X chromosome (X-linked mental retardation). X-linked mental retardation is a genetically heterogeneous condition. This is particularly true for the non-syndromic form (MRX), where MR is the only consistent clinical finding and no distinctive features between patients exist. In this situation the only possibility to group patients from different families is represented by linkage analysis, which needs the availability of large families. However, families linked to the same region demonstrate different causative genes. In these conditions, the number of patients available for analysis is a discriminating factor since a large number of patients need to be tested in order to fully confirm or exclude the involvement of a gene in MRX. # Other. This section of the bank contains biological materials and clinical data of patients with other genetic disorders (different from Rett and X-linked mental retardation). Part of this section is dedicated to Alport syndrome. Services: * Isolation of leukocytes from human peripheral blood samples * Establishment of EBV transformed lymphoblastoid cell lines from human peripheral blood leukocytes. * DNA extraction. * Plasma isolation. * Storage: ** Cryo-preservation of transformed cell lines and primary leukocytes at 135��C ** Storage of DNA at 20 degrees C ** Storage of plasma at 20 degrees C * Distribution of the stored biological samples.

Proper citation: Italian Rett Syndrome database (RRID:SCR_002000) Copy   

•   Source: SciCrunch Registry