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http://www.pierroton.inra.fr/genetics/labo/Software/Famoz/index.html

Software application that uses likelihood calculation and simulation to perform parentage studies with codominant, dominant, cytoplasmic markers or combinations of the different types (entry from Genetic Analysis Software)

Proper citation: FAMOZ (RRID:SCR_007477) Copy   

•   Source: SciCrunch Registry

http://www.mds.qmw.ac.uk/statgen/dcurtis/software.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 5th,2023. Software application that uses Monte Carlo method for assessing significance of a case-control association study with multi-allelic marker. (entry from Genetic Analysis Software).

Proper citation: CLUMP (RRID:SCR_007476) Copy   

•   Source: SciCrunch Registry

http://darwin.uvigo.es/software/treescan.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. Software application that is intended to provide p-values for the hypothesis of association between evolutionary clades and continuous traits, using haplotype trees. (entry from Genetic Analysis Software)

Proper citation: TREESCAN (RRID:SCR_007108) Copy   

•   Source: SciCrunch Registry

http://pngu.mgh.harvard.edu/purcell/whap/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 24, 2015. This package is no longer supported. The majority of the functionality for conditional haplotype tests in population-based samples has been implemented in PLINK, with a better interface and more robust, faster computation: please use that from now on. Software tool to perform haplotype-based association analysis, for quantitative and qualitative traits, in population and family samples, using single nucleotide polymorphism or multiallelic marker data. What whap can do: * Analyze quantitative and qualitative traits * Handle unrelated individuals and/or parent-offspring trio data * Perform a regression-based haplotype association test for SNP data * Perform a secondary test based on pairwise haplotype similarity * Phase genotype data using a standard E-M approach, and handle ambiguity in E-M inferred haplotypes * Include covariates and moderator variables * Flexibly constrain effects across haplotypes to tested nested models * Perform a robust within-family test when parental genotypes are present * Analyze multiallelic markers (new) * Use dominant or recessive (new) genetic models (new)

Proper citation: Whap (RRID:SCR_007103) Copy   

•   Source: SciCrunch Registry

http://www.incf.org/newsroom

Find all news and updates about INCF and neuroinformatics in the International Neuroinformatics Coordinating Facility (INCF) Newsroom.

Proper citation: INCF Newsroom (RRID:SCR_006493) Copy   

•   Source: SciCrunch Registry

http://mga.bionet.nsc.ru/soft/mgamapf2/

Software application that map QTLs in F-2 intercross in model organisms (entry from Genetic Analysis Software)

Proper citation: MGA-MAPF2 (RRID:SCR_008108) Copy   

•   Source: SciCrunch Registry

http://openccdb-dev-web.crbs.ucsd.edu/software/index.shtm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 4th,2023. Software application that is a web-based tool for viewing and annotating images. The application is based on the open source Google Web Toolkit (GWT) version 1.7, which generates Javascript code that runs on the user''s web browser. No special installation or software other than a Javascript-enabled web browser is required for use. Images to be viewed or annotated are preprocessed into multi-resolution tiles by either the commercial Zoomify preprocessor application or a locally written `zoomify_create'' tool, which produces lossless Portable Network Graphics (PNG) tiles. The WebImageBrowser application reads and manages tiled images in a manner similar to Google Maps or similar applications, allowing viewing of images of arbitrarily large size. The source code is available at https://github.com/OpenCCDB/WebImageBrowser . It requires a build. If you want the annotation function to be enabled, then you will need to install the CCDB schema in the Postgres database.

Proper citation: WebImageBrowser (RRID:SCR_007015) Copy   

•   Source: SciCrunch Registry

http://www.uni-bonn.de/~umt70e/soft.htm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 5th,2023. Software application for calculation of the restricted likelihood-ratio affected sib-pair test for linkage allowing for imprinting (entry from Genetic Analysis Software)

Proper citation: ILR (RRID:SCR_007895) Copy   

•   Source: SciCrunch Registry

http://ki.se/ki/jsp/polopoly.jsp?d=29332&a=103697&l=en

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 3rd,2023. Recently it has been discovered that specific Single Nucleotide Polymorphisms (SNPs) may elevate the risk of developing prostate cancer. This study aims at investigating whether it is possible to use these SNPs in a clinical setting in order to sharpen the diagnostic tools when investigating if a man has prostate cancer. By collecting blood from men who have undergone a needle biopsy of the prostate and do a SNP analysis of their genes and compare this with the result of the biopsy and PSA result we hope to be able to develop a test that is more specific than the routine that is being used today. Sample types: * EDTA whole blood * DNA Number of sample donors: 5321 (June 2010)

Proper citation: SPSAC - Stockholm PSA Cohort (RRID:SCR_006042) Copy   

•   Source: SciCrunch Registry

http://csg.sph.umich.edu/boehnke/sibmed.php

Software application that identifies likely genotyping errors and mutations for a sib pair in the context of multipoint mapping. (entry from Genetic Analysis Software)

Proper citation: SIBMED (RRID:SCR_007495) Copy   

•   Source: SciCrunch Registry

http://ki.se/ki/jsp/polopoly.jsp?d=29346&a=103574&l=en

THIS RESOURCE IS NO LONGER IN SERVICE, documented September 2, 2016. Cardiovascular disease and periodontitis are common diseases, causing considerable suffering and costs. Despite strong links between the two diseases it is unclear if periodontitis causes cardiovascular disease. The primary aims are to investigate whether periodontitis is a risk factor for the development of myocardial infarction and if periodontitis increases the risk for new cardiovascular events such as myocardial infarction, stroke and death in patients with a previous myocardial infarction. PAROKRANK is a case control study. Cases (n=1500) are patients with a first myocardial infarction and controls population derived people without cardiovascular disease(n=1500). Both groups are subjected to predefined dental examinations, analyses of a variety of risk factors and a biobank of blood and dental samples will be established. Information is collected from available registries (RIKS-HIA and SEPHIA) and study specific records.

Proper citation: KI Biobank - PAROKRANK (RRID:SCR_006045) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.ua.pt/coeus/

A semantic web-powered knowledge management framework, aiming at a streamlined application development cycle and following a semantic web in a box approach. The framework provides a single package including advanced data integration and triplification tools, base ontologies, a web-oriented engine and a flexible exploration API. Resources can be integrated from heterogeneous sources, including CSV and XML files or SQL and SPARQL query results, and mapped directly to one or more ontologies. Advanced interoperability features include REST services, a SPARQL endpoint and LinkedData publication. These enable the creation of multiple applications for web, desktop or mobile environments, and empower a new knowledge federation layer. It is targeted at rapid application deployment of new applications in any research field, supported by a comprehensive integration engine and an advanced data distribution API.

Proper citation: COEUS (RRID:SCR_006287) Copy   

•   Source: SciCrunch Registry

http://www.mapmanager.org/mmQT.html

A graphic, interactive program to map quantitative trait loci by regression methods; MAP MANAGER CLASSIC enhanced by quantitative trait mapping. (entry from Genetic Analysis Software)

Proper citation: MAP MANAGER QT (RRID:SCR_008101) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/Projects/D_rerio/zmp/

Create knockout alleles in protein coding genes in the zebrafish genome, using a combination of whole exome enrichment and Illumina next generation sequencing, with the aim to cover them all. Each allele created is analyzed for morphological differences and published on the ZMP site. Transcript counting is performed on alleles with a morphological phenotype. Alleles generated are archived and can be requested from this site through the Zebrafish International Resource Center (ZIRC). You may register to receive updates on genes of interest, or browse a complete list, or search by Ensembl ID, gene name or human and mouse orthologue.

Proper citation: ZMP (RRID:SCR_006161) Copy   

•   Source: SciCrunch Registry

https://scicrunch.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented September 15, 2017. Software application (entry from Genetic Analysis Software)

Proper citation: S (RRID:SCR_007646) Copy   

•   Source: SciCrunch Registry

http://www.chgb.org.cn/lda/lda.htm

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. A Java program for analyzing the pairwise linkage disequilibrium.

Proper citation: LDA (RRID:SCR_007527) Copy   

•   Source: SciCrunch Registry

http://www.mousephenotype.org/

Center that produces knockout mice and carries out high-throughput phenotyping of each line in order to determine function of every gene in mouse genome. These mice will be preserved in repositories and made available to scientific community representing valuable resource for basic scientific research as well as generating new models for human diseases.

Proper citation: International Mouse Phenotyping Consortium (IMPC) (RRID:SCR_006158) Copy   

•   Source: SciCrunch Registry

http://mcx.sf.net/mmc/

A Monte Carlo (MC) solver for photon migration in 3D turbid media. Different from existing MC software designed for layered (such as MCML) or voxel-based media (such as MMC or tMCimg), MMC can represent a complex domain using a tetrahedral mesh. This not only greatly improves the accuracy of the solutions when modeling objects with smooth/complex boundaries, but also gives an efficient way to sample the problem domain to use less memory. The current version of MMC support multi-threaded programming and can give a almost proportional speed-up when using multiple CPU cores.

Proper citation: Mesh-based Monte Carlo (MMC) (RRID:SCR_006950) Copy   

•   Source: SciCrunch Registry

http://gocognitive.net/

Free access to materials for students, educators, and researchers in cognitive psychology and cognitive neuroscience. Currently there are about a dozen demonstrations and more than 30 videos that were produced over the last two years. The basic philosophy of goCognitive rests on the assumption that easy and free access to high-quality content will improve the learning experience of students and will enable more students to enjoy the field of cognitive psychology and cognitive neuroscience. There are a few parts of goCognitive that are only available to registered users who have provided their email address, but all of the online demonstrations and videos are accessible to the everyone. Both new demonstrations and new video interviews will continually be added to the site. Manuals for each of the demonstration are being created and available as pdf files for download. Most of the demonstrations are pretty straightforward - but in some cases, especially if you would like to collect data - it might be a good idea to look over the manual. There are different ways in which you can get involved and contribute to the site. Your involvement can range from sending us feedback about the demonstrations and videos, suggestions for new materials, or the simple submission of corrections, to the creation or publication of demonstrations and videos that meet our criteria. Down the road we will make the submission process easier, but for now please contact swerner (at) uidaho dot edu for more information. NSF student grant Undergraduate students can apply through goCognitive for an $1,100 grant to co-produce a new video interview with a leading researcher in the field of cognitive neuroscience. The funding has been provided by the National Science Foundation.

Proper citation: goCognitive (RRID:SCR_006154) Copy   

•   Source: SciCrunch Registry

http://biomail.sourceforge.net/biomail/

BioMail is a small web-based application for medical researchers, biologists, and anyone who wants to know the latest information about a disease or a biological phenomenon. It is written to automate searching for recent scientific papers in the PubMed Medline database. BioMail is free and will stay free. What does BioMail do? Periodically BioMail does a user-customized Medline search and sends all matching articles recently added to Medline to the users'' e-mail address. HTML-formatted e-mails generated by BioMail can be used to view selected references in medline format (compatible with most reference manager programs). Why is BioMail helpful? If you use Medline, it may be hard to remember when you did your last search. Often you must scan titles you have already seen to be certain you didn''t miss an important reference. BioMail will perform routine searches for you. This program alerts users to all new papers in their fields automatically. It also helps the user to ''refine'' search patterns once and for all. There is no need to wonder: ''What was that great search pattern I used last Saturday?''. All patterns are safe in the database and can be accessed, tuned, or deleted any time. It is also useful for countries where access to the Internet is not yet widely available. If a person has a permanent e-mail address, but only sporadic www access, she/he only needs to fill out a BioMail form once and then will receive new references from Medline continually.

Proper citation: BioMail (RRID:SCR_008174) Copy   

•   Source: SciCrunch Registry