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http://cbrain.mcgill.ca/loris

A modular and extensible web-based data management system that integrates all aspects of a multi-center study, from heterogeneous data acquisition to storage, processing and ultimately dissemination, within a streamlined platform. Through a standard web browser, users are able to perform a wide variety of tasks, such as data entry, 3D image visualization and data querying. LORIS also stores data independently from any image processing pipeline, such that data can be processed by external image analysis software tools. LORIS provides a secure web-based and database-driven infrastructure to automate the flow of clinical data for complex multi-site neuroimaging trials and studies providing researchers with the ability to easily store, link, and access significant quantities of both scalar (clinical, psychological, genomic) and multi-dimensional (imaging) data. LORIS can collect behavioral, neurological, and imaging data, including anatomical and functional 3D/4D MRI models, atlases and maps. LORIS also functions as a project monitoring and auditing platform to oversee data acquisition across multiple study sites. Confidentiality during multi-site data sharing is provided by the Subject Profile Management System, which can perform automatic removal of confidential personal information and multiple real-time quality control checks. Additionally, web interactions with the LORIS portal take place over an encrypted channel via SSL, ensuring data security. Additional features such as Double Data Entry and Statistics and Data Query GUI are included.

Proper citation: LORIS - Longitudinal Online Research and Imaging System (RRID:SCR_000590) Copy   

•   Source: SciCrunch Registry
  

https://github.com/feizhe/PGS

Software tool for association study of high-dimensional microRNA expression data with repeated measures. The penalized regression model incorporates a grid search method for analyzing associations of high-dimensional microRNA expression data with repeated measures.

Proper citation: PGS (RRID:SCR_000475) Copy   

•   Source: SciCrunch Registry
  

http://parsecnv.sourceforge.net/

Software that takes CNV calls as input and creates SNP based statistics for CNV occurrence in cases and controls then calls CNVRs based on neighboring SNPs of similar significance.

Proper citation: ParseCNV (RRID:SCR_000355) Copy   

•   Source: SciCrunch Registry
  

http://purl.bioontology.org/ontology/DOID

Comprehensive hierarchical controlled vocabulary for human disease representation.Open source ontology for integration of biomedical data associated with human disease. Disease Ontology database represents comprehensive knowledge base of inherited, developmental and acquired human diseases.

Proper citation: Human Disease Ontology (RRID:SCR_000476) Copy   

•   Source: SciCrunch Registry
  

http://trace.ddbj.nig.ac.jp/dor/index_e.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Archival database of functional genomics data generated by microarray and highly parallel new generation sequencers. Data are exchanged between ArrayExpress at EBI and DOR in common MAGE-TAB format. Supports MIAME and MINSEQE-compliant data submissions. DOR issues accession numbers, E-DORD-n to experiment and A-DORD-n to array design. DOR exchanges public data with the EBI ArrayExpress in common MAGE-TAB format. Note: At present, DOR does not accept submissions. DDBJ will announce launch of DOR when it is ready. (2013/01/31) The data can be kept private until your paper is published. You can set the hold date for a maximum of 1 year and can change it. Registered records are released according to the Data Release Policy.

Proper citation: DDBJ Omics Archive (RRID:SCR_000597) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/kinannote/

Software that identifies and classifies protein kinases in a user-provided fasta file using an HMM derived from serine / threonine protein kinases, a position specific scoring matrix derived from the HMM, and comparison with a local version of the curated kinase database from kinase.com.

Proper citation: Kinannote (RRID:SCR_000352) Copy   

•   Source: SciCrunch Registry
  

http://purl.bioontology.org/ontology/GAZ

THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 23, 2014. Description not available.

Proper citation: Gazetteer (RRID:SCR_000473) Copy   

•   Source: SciCrunch Registry
  

http://www.scienceexchange.com/facilities/genomics-services-lab

A lab that offers genetic research tools such as RNA sequencing and a variety of arrays.

Proper citation: HudsonAlpha Genomics Services Lab (RRID:SCR_000353) Copy   

•   Source: SciCrunch Registry
  

http://www.du.edu/psychology/

The department of psychology at Denver University that offers degrees at the undergraduate, graduate and doctoral level. The doctoral programs have specializations such as Affect/Social, Child Clinical, Cognitive, and Developmental.

Proper citation: Denver University Department of Psychology (RRID:SCR_000474) Copy   

•   Source: SciCrunch Registry
  

http://www.broadinstitute.org/cancer/cga/contest

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 8,2025. A software tool (and method) for estimating the amount of cross-sample contamination in next generation sequencing data.

Proper citation: ContEst (RRID:SCR_000595) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/jnomics/

A collection of cloud-scale DNA sequence analysis tools.

Proper citation: Jnomics (RRID:SCR_000348) Copy   

•   Source: SciCrunch Registry
  

https://github.com/cc2qe/speedseq

Software for a lightweight, flexible, and open source pipeline that identifies genomic variation (single nucleotide variants (SNVs), indels, and structural variants (SVs)).

Proper citation: SpeedSeq (RRID:SCR_000469) Copy   

•   Source: SciCrunch Registry
  

http://www.abrowse.org/

A genome browser framework which gives an open browsing experience, open data access, collaborative work support, and a framework to import annotations. Multiple data access approaches are supported for external platforms to retrieve data from ABrowse. This resource also contains an online user-space in which users can create, store and share comments, annotations and landmarks.

Proper citation: ABrowse (RRID:SCR_000345) Copy   

•   Source: SciCrunch Registry
  

http://www.hl7.org/index.cfm?ref=nav

ANSI-accredited standards developing organization providing a comprehensive framework and related standards for the exchange, integration, sharing, and retrieval of electronic health information that supports clinical practice and the management, delivery and evaluation of health services. HL7's 2,300+ members include approximately 500 corporate members who represent more than 90% of the information systems vendors serving healthcare. HL7 provides standards for interoperability that improve care delivery, optimize workflow, reduce ambiguity and enhance knowledge transfer among all of their stakeholders, including healthcare providers, government agencies, the vendor community, fellow SDOs and patients.

Proper citation: Health Level Seven International (RRID:SCR_000466) Copy   

•   Source: SciCrunch Registry
  

http://www.atgc-montpellier.fr/mpscan/

Web tool for index free mapping of multiple short reads on a genome.

Proper citation: MPscan (RRID:SCR_000587) Copy   

•   Source: SciCrunch Registry
  

http://icbi.at/software/gpviz/gpviz.shtml

A versatile Java-based software used for dynamic gene-centered visualization of genomic regions and/or variants.

Proper citation: GPViz (RRID:SCR_000346) Copy   

•   Source: SciCrunch Registry
  

http://teddy.epi.usf.edu/

International consortium of six centers assembled to participate in the development and implementation of studies to identify infectious agents, dietary factors, or other environmental agents, including psychosocial factors, that trigger type 1 diabetes in genetically susceptible people. The coordinating centers recruit and enroll subjects, obtaining informed consent from parents prior to or shortly after birth, genetic and other types of samples from neonates and parents, and prospectively following selected neonates throughout childhood or until development of islet autoimmunity or T1DM. The study tracks child diet, illnesses, allergies and other life experiences. A blood sample is taken from children every 3 months for 4 years. After 4 years, children will be seen every 6 months until the age of 15 years. Children are tested for 3 different autoantibodies. The study will compare the life experiences and blood and stool tests of the children who get autoantibodies and diabetes with some of those children who do not get autoantibodies or diabetes. In this way the study hopes to find the triggers of T1DM in children with higher risk genes.

Proper citation: TEDDY (RRID:SCR_000383) Copy   

•   Source: SciCrunch Registry
  

http://www.tarp.nih.gov/

Trans-NIH program encouraging and facilitating the study of the underlying mechanisms controlling blood vessel growth and development. Other aims include: to identify specific targets and to develop therapeutics against pathologic angiogenesis in order to reduce the morbidity due to abnormal blood vessel proliferation in a variety of disease states; to better understand the process of angiogenesis and vascularization to improve states of decreased vascularization; to encourage and facilitate the study of the processes of lymphangiogenesis; and to achieve these goals through a multidisciplinary approach, bringing together investigators with varied backgrounds and varied interests.

Proper citation: Trans-Institute Angiogenesis Research Program (RRID:SCR_000384) Copy   

•   Source: SciCrunch Registry
  

https://sunnylab.wordpress.com/about/

An antibody supplier that provides a range of human antigens, serum and plasma, and cell culture reagents.

Proper citation: SunnyLab (RRID:SCR_000382) Copy   

•   Source: SciCrunch Registry
  

http://www.massachusetts.edu/index.html

A five-campus public university system in Massachusetts. The system includes four universities, a medical school, and a satellite campus.

Proper citation: University of Massachusetts; Massachusetts; USA (RRID:SCR_000379) Copy   

•   Source: SciCrunch Registry