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http://www.lead-dbs.org/

MATLAB toolbox for deep-brain-stimulation (DBS) electrode reconstructions and visualizations based on postoperative MRI and computed tomography (CT) imaging. The toolbox also facilitates visualization of localization results in 2D/3D, analysis of DBS-electrode placement's effects on clinical results, simulation of DBS stimulations, diffusion tensor imaging (DTI) based connectivity estimates, and fiber-tracking from the VAT to other brain regions (connectomic surgery).

Proper citation: LEAD-DBS (RRID:SCR_002915) Copy   

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http://www.roswellpark.edu/shared-resources/data-bank-and-biorepository

Collects and provides de-identified biospecimens and associated epidemiological and clinical data to meet the scientific needs of investigators. Newly diagnosed patients are asked to contribute data and specimens to the DBBR prior to treatment. Other patients with who have benign disease or advanced disease and have undergone treatment are also enrolled based on anticipated use of data and samples for research. Additionally, non-patients (family members and friends of patients and community members) with no personal history of cancer are asked to participate in the biorepository as controls. Specimens and data are procured with protected health information (PHI) and de-identified prior to distribution to investigators with hypothesis driven IRB reviewed studies. An extensive data collection and management system is in place to track informed consent, questionnaire collection and follow up, epidemiological questionnaire data, clinical data, biospecimens and their derivatives. Research Services * Availability of a bank of prospectively collected blood specimens (serum, plasma, buffy coat, red blood cells and DNA) from cancer patients, high risk individuals and healthy controls for research. * Collection, linking and distribution of epidemiologic and clinical data with biospecimens. * Study-specific biospecimen and data procurement to meet the needs of individual studies, including: ** Participant identification, eligibility screening and informed consent ** Serial biospecimen procurement prior to and throughout treatment ** Study specific collection of biospecimens other than blood (buccal cells, sputum, and urine) ** Procurement and distribution of fresh biospecimens ** Collection of extended clinical and risk factor data

Proper citation: Roswell Park Data Bank and BioRepository (RRID:SCR_003607) Copy   

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http://microarray.ym.edu.tw:8080/tools/module/set/index.jsp?mode=home

A Java tool to evaluate and visualize the sample discrimination abilities of gene expression signatures. This tool provides a filtration function for signature identification and lies between clinical analyses and class prediction (or feature selection) tools.

Proper citation: SET (RRID:SCR_003605) Copy   

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https://www.signalingpathways.org/ominer/query.jsf

THIS RESOURCE IS NO LONGER IN SERVICE.Documented on February 25, 2022.Software tool as knowledge environment resource that accrues, develops, and communicates information that advances understanding of structure, function, and role in disease of nuclear receptors (NRs) and coregulators. It specifically seeks to elucidate roles played by NRs and coregulators in metabolism and development of metabolic disorders. Includes large validated data sets, access to reagents, new findings, library of annotated prior publications in field, and journal covering reviews and techniques.As of March 20, 2020, NURSA is succeeded by the Signaling Pathways Project (SPP).

Proper citation: Nuclear Receptor Signaling Atlas (RRID:SCR_003287) Copy   

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http://openmeeg.gforge.inria.fr

A C++ package for low-frequency bio-electromagnetism solving forward problems in the field of EEG and MEG with very high accuracy.

Proper citation: OpenMEEG (RRID:SCR_002510) Copy   

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http://www.ebi.ac.uk/Tools/

The European Bioinformatics Institute (EBI) toolbox area provides a comprehensive range of tools for the field of bioinformatics. These are subdivided into categories in the left menu for convenience. EBI has developed a large number of very useful bioinformatics tools. A few examples include: - Similarity & Homology - the BLAST or FASTA programs can be used to look for sequence similarity and infer homology. - Protein Functional Analysis - InterProScan can be used to search for motifs in your protein sequence. - Proteomic Services NEW - UniProt DAS server allows researchers to show their research results in the context of UniProtKB/Swiss-Prot annotation. - Sequence Analysis - ClustalW2 a sequence alignment tool. - Structural Analysis - MSDfold can be used to query your protein structure and compare it to those in the Protein Data Bank (PDB). - Web Services - provide programmatic access to the various databases and retrieval/analysis services EBI provides. - Tools Miscellaneous - Expression Profiler a set of tools for clustering, analysis and visualization of gene expression and other genomic data. Sponsors: This resource is sponsored by EBI.

Proper citation: Toolbox at the European Bioinformatics Institute (RRID:SCR_002872) Copy   

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http://psychology-tools.com/cast/

Assessment test developed by the Autism Research Centre at the University of Cambridge, for assessing the severity of autism spectrum symptoms in children. This assessment is usually used with children aged from 4-11 years of age.

Proper citation: Childhood Autism Spectrum Test (RRID:SCR_003322) Copy   

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http://www.crl.med.harvard.edu/software/STAPLE/index.php

An algorithm for the Simultaneous Truth and Performance Level Estimation, which estimates a reference standard and segmentation generator performance from a set of segmentations. It has been widely applied for the validation of image segmentation algorithms, and to compare the performance of different algorithms and experts. It has also found application in the identification of a consensus segmentation, by combination of the output of a group of segmentation algorithms, and for segmentation by registration and template fusion., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: STAPLE (RRID:SCR_002590) Copy   

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https://en.wikipedia.org/wiki/SharedCopy

THIS RESOURCE IS NO LONGER IN SERVICE, documented on May 12, 2017. Web application for annotation and collaboration on web pages. Its features include the ability to highlight words, comment, and share annotated copies of the web page that can be annotated by other users.

Proper citation: SharedCopy (RRID:SCR_002867) Copy   

•   Source: SciCrunch Registry

http://nipy.org/nipype/

A package for writing fMRI analysis pipelines and interfacing with external analysis packages (SPM, FSL, AFNI). Current neuroimaging software offer users an incredible opportunity to analyze their data in different ways, with different underlying assumptions. However, this has resulted in a heterogeneous collection of specialized applications without transparent interoperability or a uniform operating interface. Nipype, an open-source, community-developed initiative under the umbrella of Nipy, is a Python project that solves these issues by providing a uniform interface to existing neuroimaging software and by facilitating interaction between these packages within a single workflow. Nipype provides an environment that encourages interactive exploration of algorithms from different packages (e.g., SPM, FSL), eases the design of workflows within and between packages, and reduces the learning curve necessary to use different packages. Nipype is creating a collaborative platform for neuroimaging software development in a high-level language and addressing limitations of existing pipeline systems.

Proper citation: Nipype (RRID:SCR_002502) Copy   

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http://www.people.fas.harvard.edu/~junliu/genotype/

Software application (entry from Genetic Analysis Software)

Proper citation: GS-EM (RRID:SCR_003992) Copy   

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http://www.edarstudy.eu/

A European collaborative study to develop and validate new biomarkers for Alzheimer's disease. Central in the project is the development of an assay for the measurement of beta amyloid oligomers in cerebrospinal fluid and plasma. In order to validate the assay for beta amyloid oligomers, cerebrospinal fluid and plasma will be repeatedly collected in subjects with Alzheimer's disease, other types of dementia, mild cognitive impairment, and control subjects.

Proper citation: EDAR study: biomarkers for Alzheimer's disease (RRID:SCR_004445) Copy   

•   Source: SciCrunch Registry

http://www.emedicinehealth.com/dementia_due_to_hiv_infection/article_em.htm

A narrative resource that provides a wealth of information on topic including: * Dementia Due to HIV Infection Overview * Dementia Due to HIV Infection Causes * Dementia Due to HIV Infection Symptoms * Exams and Tests * Dementia Due to HIV Infection Treatment * Self-Care at Home * Medical Treatment * Next Steps * Follow-up * Prevention * Outlook * Support Groups and Counseling * For More Information * Web Links * Multimedia * Synonyms and Keywords Additional information includes: * HIV AIDS Myths and Facts Slideshow Pictures * Take the HIV/AIDS Quiz * AIDS Retrospective Slideshow Pictures

Proper citation: emedicinehealth: Dementia Due to HIV Infection (RRID:SCR_004566) Copy   

•   Source: SciCrunch Registry

http://www.kcl.ac.uk/ioppn/depts/neuroimaging/research/imaginganalysis/Software/PIPR.aspx

Software toolbox designed to provide machine learning methods for pre-processed imaging data allowing for two (or more) class classification in the context of drug development. The Toolbox includes implementations of Gaussian Process Classification, Support Vector Machines, Ordinal Regression and Sparse Multinomial Logistic Regression for fMRI, Structural and ASL imaging data.

Proper citation: Pharmacological Imaging and Pattern Recognition toolbox (RRID:SCR_003874) Copy   

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http://www.ohsu.edu/xd/research/centers-institutes/octri/current-projects/ohsu-biolibrary/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023.A Joint Project between Oregon Clinical and Translational Research Institute (OCTRI) and the Knight Cancer Institute, the OHSU Biolibrary provides information on campus collections of biospecimens originating from OHSU patients. The Biolibrary Search Engine is a user-friendly, online search tool that allows OHSU researchers to search for suitable biospecimen samples. As of October 2010, the Biolibrary Search Engine contains data on over 500,000 biospecimens. The Search Engine accesses data from the OHSU Cancer Registry, the Department of Pathology, and the OCTRI Research Data Warehouse. You must be connected to the OHSU network to access the Search Engine. The Search Engine is accessible on Internet Explorer through WTS connection to the OHSU network.

Proper citation: OHSU Biolibrary (RRID:SCR_004282) Copy   

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http://www.hipsci.org/

A UK national induced pluripotent stem (iPS) cell resource that will create and characterize more than 1000 human iPSCs from healthy and diseased tissue for use in cellular genetic studies. Between 2013 and 2016 they aim to generate iPS cells from over 500 healthy individuals and 500 individuals with genetic disease. They will then use these cells to discover how genomic variation impacts on cellular phenotype and identify new disease mechanisms. Strong links with NHS investigators will ensure that studies on the disease-associated cell lines will be linked to extensive clinical information. Further key features of the project are an open access model of data sharing; engagement of the wider clinical genetics community in selecting patient samples; and provision of dedicated laboratory space for collaborative cell phenotyping and differentiation.

Proper citation: HipSci (RRID:SCR_003909) Copy   

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http://www.medtronic.com/

Medical technology company that develops and manufactures devices and therapies to treat more than 30 chronic diseases, including heart failure, Parkinson's disease, urinary incontinence, Down syndrome, obesity, chronic pain, spinal disorders, and diabetes. A Commercial healthcare organization for both patients and healthcare professionals. For professionals, it provides products, therapy and procedure solutions, and services.

Proper citation: Medtronic (RRID:SCR_003988) Copy   

•   Source: SciCrunch Registry

http://www.ibcresearch.org/biobank/

The IBC Research Foundation BioBank is a secure, privacy-protected collection of biological specimens from ibc-diagnosed patients (cases, and, unlike the former George Washington University IBC Registry, ibc patients who have died, those who are under legal age, and those living but unable to make decisions for themselves, may be consented to participate in the IBC Research Foundation BioBank by their authorized representative) and from those not diagnosed with ibc (controls), volunteering following a consent decision making process, and signing an Informed Consent. Clinical Data and a comprehensive questionnaire will also be obtained for those diagnosed with ibc. The Inflammatory Breast Cancer Research Foundation (ibcRF) has established a BioBank and Clinical Database. The BioBank contains non-tumor RNA and DNA, tumor RNA and DNA, blocks and slides from diagnostic pathology, and medical records describing clinical and pathologic findings at diagnosis.

Proper citation: Inflammatory Breast Cancer Biobank (RRID:SCR_004556) Copy   

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http://vitiligobiobank.org/

A non-profit collection of biological samples and detailed associated clinical data, designed to facilitate medical research into vitiligo, a devastating skin disease that is much neglected. They collect, store and analyze biological samples throughout the network of collaborators in 11 countries, using standard collection protocols and unified patient record, which are then made available to the scientific community and research organizations investigating pathogeneses, diagnostics, new treatments, and ultimately a cure for vitiligo. The core asset is a large collection of well-organized hair, blood, serum and DNA samples, integrated with comprehensive and anonymized patient records.

Proper citation: Vitiligo Biobank (RRID:SCR_003863) Copy   

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http://www.bonebank.com

Bone Bank Allografts is the distributor of the SteriGraft line of high quality bone and soft tissue allografts to medical professionals. The company has been in existence for over 13 years and has helped doctors and their patients with over one hundred thousand successful transplantations. Bone and soft tissue allografts in the SteriGraft line are validated to a sterility assurance level (SAL) of 10(-6) in accordance with ISO 11137-2 Method 1. Bone Bank Allografts was founded in 1993 in response to a growing need for allograft tissue in South Texas. Since 1993, Bone Bank Allografts'' distribution network has grown to cover Texas, the country and the globe, fulfilling surgical needs for allograft tissue in more than 175,000 successful transplantations. Located in San Antonio, Texas, Bone Bank Allografts is dedicated to a just, equitable and fair distribution of cadaveric tissue to surgeons, hospitals, surgicenters and dental offices. Over the years, our customers have come to rely on the superior quality of our tissue products as well as the unmatched service of our well trained, certified Tissue Bank Specialists (CTBS) and our knowledgeable distribution staff. With accreditation from the American Association of Tissue Banks (AATB), registration with the U.S. Food and Drug Administration (FDA) and compliance with the FDA''s Good Tissue Practices, Bone Bank Allografts continues to pursue our mission: To enhance the quality of patient care by providing safe, high quality allograft tissues to health care professionals for transplant and research. Most recently, Bone Bank Allografts has taken the next important step in tissue banking by developing a powerful partnership with Texas Human Biologics (THB) in order to process donated human tissue.

Proper citation: Bone Bank Allografts (RRID:SCR_004432) Copy   

•   Source: SciCrunch Registry