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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

http://khmer.readthedocs.org/

Software library and suite of command line tools for working with DNA sequence that takes a k-mer-centric approach to sequence analysis. It is primarily aimed at short-read sequencing data such as that produced by the Illumina platform.

Proper citation: khmer (RRID:SCR_001156) Copy   

•   Source: SciCrunch Registry

http://www.speedbiosystems.com/

Commercial antibody supplier based in Maryland.

Proper citation: Speed BioSystems (RRID:SCR_001673) Copy   

•   Source: SciCrunch Registry

http://bmsr.usc.edu/software/targetgene/

MATLAB tool to effectively identify potential therapeutic targets and drugs in cancer using genetic network-based approaches. It can rapidly extract genetic interactions from a precompiled database stored as a MATLAB MAT-file without the need to interrogate remote SQL databases. Millions of interactions involving thousands of candidate genes can be mapped to the genetic network within minutes. While TARGETgene is currently based on the gene network reported in (Wu et al.,Bioinformatics 26:807-813, 2010), it can be easily extended to allow the optional use of other developed gene networks. The simple graphical user interface also enables rapid, intuitive mapping and analysis of therapeutic targets at the systems level. By mapping predictions to drug-target information, TARGETgene may be used as an initial drug screening tool that identifies compounds for further evaluation. In addition, TARGETgene is expected to be applicable to identify potential therapeutic targets for any type or subtype of cancers, even those rare cancers that are not genetically recognized. Identification of Potential Therapeutic Targets * Prioritize potential therapeutic targets from thousands of candidate genes generated from high-throughput experiments using network-based metrics * Validate predictions (prioritization) using user-defined benchmark genes and curated cancer genes * Explore biologic information of selected targets through external databases (e.g., NCBI Entrez Gene) and gene function enrichment analysis Initial Drug Screening * Identify for further evaluation existing drugs and compounds that may act on the potential therapeutic targets identified by TARGETgene * Explore general information on identified drugs of interest through several external links Operating System: Windows XP / Vista / 7

Proper citation: TARGETgene (RRID:SCR_001392) Copy   

•   Source: SciCrunch Registry

http://www.ijs.si/ijsw/JSI

A scientific research institute that is involved with a broad spectrum of basic and applied research. Some of the areas they focus on include production and control technologies, communication and computer technology, and energy utilization and environmental science. They also engage in collaborations to develop medical equipment and new diagnostic methods into clinical medicine.

Proper citation: Jozef Stefan Institute; Ljubljana; Slovenia (RRID:SCR_000974) Copy   

•   Source: SciCrunch Registry

http://faculty.washington.edu/browning/beagle/beagle.html

Software package for analysis of large-scale genetic data sets with hundreds of thousands of markers genotyped on thousands of samples. BEAGLE can * phase genotype data (i.e. infer haplotypes) for unrelated individuals, parent-offspring pairs, and parent-offspring trios. * infer sporadic missing genotype data. * impute ungenotyped markers that have been genotyped in a reference panel. * perform single marker and haplotypic association analysis. * detect genetic regions that are homozygous-by-descent in an individual or identical-by-descent in pairs of individuals. Beagle can also be used in conjunction with PRESTO, a program for fast and flexible permutation testing. PRESTO can compute empirical distributions of order statistics, analyze stratified data, and determine significance levels for one-stage and two-stage genetic association studies. BEAGLE is written in Java and runs on any computing platform with a Java version 1.6 interpreter (e.g. Windows, Unix, Linux, Solaris, Mac).

Proper citation: BEAGLE (RRID:SCR_001789) Copy   

•   Source: SciCrunch Registry

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

Software R package to model and impute non-detects in results of qPCR experiments.Used to directly model non-detects as missing data.

Proper citation: nondetects (RRID:SCR_001702) Copy   

•   Source: SciCrunch Registry

https://www.apbenson.com/cyrillic-downloads

Software application for pedigree drawing with fully integrated risk analysis and support for industry standard databases (MS Access and Corel Paradox). It is designed for genetic counselors and others who work with patients. Cyrillic 2 draws pedigrees, works with genetic marker data, lets you do haplotyping and allows exports to a range of linkage analysis packages.

Proper citation: CYRILLIC (RRID:SCR_001823) Copy   

•   Source: SciCrunch Registry

http://www.zfishbook.org/NGP/journalcontent/SCORE/SCORE.html

Narrative resource describing a visual data analysis and collection approach that takes advantage of the cylindrical nature of the zebrafish allowing for an efficient and effective method for image capture called, Specimen in a Corrected Optical Rotational Enclosure (SCORE) Imaging. To achieve a non-distorted image, zebrafish were placed in a fluorinated ethylene propylene (FEP) tube with a surrounding, optically corrected imaging solution: water. By similarly matching the refractive index of the housing (FEP tubing) to that of the inner liquid and outer liquid (water), distortion was markedly reduced, producing a crisp imagable specimen that is able to be fully rotated 360 degrees. A similar procedure was established for fixed zebrafish embryos using convenient, readily available borosilicate capillaries surrounded by 75% glycerol. The method described could be applied to chemical genetic screening and other, related high-throughput methods within the fish community and among other scientific fields.

Proper citation: Zebrafish - SCORE Imaging: Specimen in a Corrected Optical Rotational Enclosure (RRID:SCR_001300) Copy   

•   Source: SciCrunch Registry

https://www.anaspec.com/

Commercial supplier of antibodies, reagents, and dyes for research.

Proper citation: AnaSpec (RRID:SCR_002114) Copy   

•   Source: SciCrunch Registry