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http://compbio.bccrc.ca/software/mutationseq/

A software suite using feature-based classifiers for somatic mutation prediction from paired tumour/normal next-generation sequencing data. mutationSeq has the advantages of integrating different features (e.g., base qualities, mapping qualities, strand bias, and tailed distance features), and validated somatic mutations to make predictions. Given paired normal/tumour bam files, mutationSeq will output the probability of each candidate site being somatic.

Proper citation: mutationSeq (RRID:SCR_006815) Copy   

•   Source: SciCrunch Registry

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

Software to estimate purity / ploidy, and from that compute absolute copy-number and mutation multiplicities. When DNA is extracted from an admixed population of cancer and normal cells, the information on absolute copy number per cancer cell is lost in the mixing. The purpose of ABSOLUTE is to re-extract these data from the mixed DNA population. This process begins by generation of segmented copy number data, which is input to the ABSOLUTE algorithm together with pre-computed models of recurrent cancer karyotypes and, optionally, allelic fraction values for somatic point mutations. The output of ABSOLUTE then provides re-extracted information on the absolute cellular copy number of local DNA segments and, for point mutations, the number of mutated alleles.

Proper citation: ABSOLUTE (RRID:SCR_005198) Copy   

•   Source: SciCrunch Registry

http://www.iro.umontreal.ca/~csuros/quadgt/

Software package for calling single-nucleotide variants in four sequenced genomes comprising a normal-tumor pair and the two parents. Genotypes are inferred using a joint model of parental variant frequencies, de novo germline mutations, and somatic mutations. The model quantifies the descent-by-modification relationships between the unknown genotypes by using a set of parameters in a Bayesian inference setting. Note that you can use it on any subset of the four related genomes, including parent-offspring trios, and normal-tumor pairs without parental samples.

Proper citation: QuadGT (RRID:SCR_000073) Copy   

•   Source: SciCrunch Registry

https://abl.azdhs.gov

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.

Proper citation: Arizona Biospecimen Locator (RRID:SCR_004151) Copy   

•   Source: SciCrunch Registry

https://ndriresource.org/for-researchers/services-capabilities-sample/htorr

NDRI’s Human Tissue and Organs for Research Resource (HTORR) Program has been funded by the National Institutes of Health (NIH) for over 30 consecutive years to support research programs across multiple disciplines. It is through the HTORR program that NDRI provides academic biomedical investigators with donated normal and diseased human tissues and organs recovered from a diverse donor pool using customized procurement, processing, and preservation and distribution protocols. Our HTORR Program supports academic biomedical research investigators needs by providing: Access to a wide array of human biospecimens from any body system * Customized procurement in a variety of preservation formats including fresh, frozen, and fixed suitable for various analytical techniques * Reduced costs for tissue procurement * Technical support to design your studies utilizing human biospecimens * Letters of support and budgetary information for grant applications

Proper citation: Human Tissue and Organ for Research Resource (HTORR) (RRID:SCR_002859) Copy   

•   Source: SciCrunch Registry

http://www.med.unc.edu/bric/ideagroup/free-softwares/unc-infant-0-1-2-atlases

3 atlases dedicated for neonates, 1-year-olds, and 2-year-olds. Each atlas comprises a set of 3D images made up of the intensity model, tissue probability maps, and anatomical parcellation map. These atlases are constructed with the help of state-of-the-art infant MR segmentation and groupwise registration methods, on a set of longitudinal images acquired from 95 normal infants (56 males and 39 females) at neonate, 1-year-old, and 2-year-old.

Proper citation: UNC Infant 0-1-2 Atlases (RRID:SCR_002569) Copy   

•   Source: SciCrunch Registry

http://www.ilsbio.com/

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone., documented on August 17, 2021.Biospecimens and support services to advance translational research including a wide range of specimen types, including matched sets of normal and diseased tissue, Formalin-Fixed, Paraffin-Embedded (FFPE), blood, and serum, focusing primarily on cancer. They stock a wide range of sample formats to help meet research goals quickly and on budget. Collections are preformed to be ideal for a wide range of studies including genomic, proteomic, molecular and histologic analysis. ILSbio provides tissue and tissue derivatives that are high quality, cost effective and procured in compliance with current and anticipated regulations. The company obtains its clinical specimens under strict IRB approved protocols with informed consent and the utmost attention to issues of patient safety, anonymity and confidentiality. Clinical and pathological data is available for all specimens. Researchers use the tissue products at all levels of scientific study ranging from large pharma and biotech organizations to small labs and university research facilities. They also participate in wholesale distribution to other bio-banking organizations.

Proper citation: ILSbio (RRID:SCR_004682) Copy   

•   Source: SciCrunch Registry

http://www.tumorbank.unibe.ch/

Tumorbank Bern - TBB collects high quality clinical samples since 2003 for translational research selected by expert pathologists under controlled conditions of normal and diseased tissue from different origin. The Tumor Bank is approved by the Ethical Commission of Bern, we only collect samples with written informed patient consent. Origin of Tissue: Thoracic Surgery, Gynecology, Urology, Visceral Surgery, Orthopedic Surgery, Head and Neck Surgery, Neurosurgery Tumorbank Bern TBB holds 12,000 samples from 3600 Patients. Please contact us to check if we have samples for your field of research.

Proper citation: Tumorbank Bern (RRID:SCR_004611) Copy   

•   Source: SciCrunch Registry

https://moffitt.org/research-science/shared-resources/tissue/

A central tissue repository at Moffitt specializing in protocol-driven human tissue collection, storage, processing and dissemination. Tissue Core provides investigators with access to high quality, well-annotated human specimens obtained from representative of the patient populations. The advent of powerful molecular technologies has opened the door to developing more effective treatments of patients with cancer. Access to high quality specimens with associated clinical, treatment, recurrence outcome data will be critical to developing and validating the tests needed for diagnosis and prediction of response to therapy. Since its commencement in 1993, the Tissue Core has collected more than 8,000 cases of human liquid cancers and solid primary and metastatic tumors both malignant and benign with adjacent normal, from variety of sites and diagnoses. Collected samples are mostly remnant tissues obtained from patients undergoing therapeutic surgical procedures at the Center. The core also ensures tissue release compliance with USF-IRB and Privacy Board recommendations. * Protocol driven sample collection, processing and distribution * Collection of sample and patient demographic information. * Nucleic acid extractions from tissue sections, FNA, core biopsies blood and bone marrow. * Histology services: H&E slides, staining, sectioning, paraffin blocks, OCT blocks, sample microdissection * WBC, plasma and serum isolation. * Project development and support: Facility staff provides advice and guidance to researchers.

Proper citation: Moffitt Cancer Center Tissue Core (RRID:SCR_004406) Copy   

•   Source: SciCrunch Registry

http://worldbiobank.net/

Founded by the physician partners of ACORN, Inc. (Accelerated Community Oncology Research Network), World BioBank embraces forward-thinking technology and a strong commitment to the advancement of bioscience. The World BioBank collects cancer samples, normal samples, and other non-neoplastic diseases. Data available include sample-specific data, patient-specific data, and study-related data. * SOLID TISSUES (snap frozen and matched formalin-fixed paraffin embedded diseased and normal internal controls) from: Surgical resections, Image-guided biopsies, Bone marrow biopsies, Endoscopic biopsies * LIQUID TISSUES: Peripheral blood, Genomic DNA (from buffy coat), Plasma, Serum World BioBank is committed to marrying samples to a wealth of longitudinal medical data and tissue-specific data.

Proper citation: World BioBank (RRID:SCR_004958) Copy   

•   Source: SciCrunch Registry

http://www.bumc.bu.edu/busm-pathology/pathology-core-services/biospecimen-archive-research-core-barc/

Biospecimen repository of normal and diseased human material from a variety of tissues and conditions along with clinical annotation. Both frozen aliquots and paraffin embedded tissue are available. Biospecimens are available to qualified researchers with IRB approval. * Preliminary inquires please contact Cheryl Spencer at cheryl.spencer (at) bmc.org

Proper citation: Boston University Biospecimen Archive Research Core (RRID:SCR_005363) Copy   

•   Source: SciCrunch Registry

http://cmrm.med.jhmi.edu/cmrm/atlas/human_data/file/JHUtemplate_newuser.html

DTI white matter atlases with different data sources and different image processing. These include single-subject, group-averaged, B0 correction, processed atlases (White Matter Parcellation Map, Tract-probability maps, Conceptual difference between the WMPM and tract-probability maps), and linear or non-linear transformation for automated white matter segmentation. # Adam single-subject white matter atlas (old version): These are electronic versions of atlases published in Wakana et al, Radiology, 230, 77-87 (2004) and MRI Atlas of Human White Matter, Elsevier. ## Original Adam Atlas: 256 x 256 x 55 (FOV = 246 x 246 mm / 2.2 mm slices) (The original matrix is 96x96x55 (2.2 mm isotropic) which is zerofilled to 256 x 256 ## Re-sliced Adam Atlas: 246 x 246 x 121 (1 mm isotropic) ## Talairach Adam: 246 x 246 x 121 (1 mm isotropic) # New Eve single-subject white matter atlas: The new version of the single-subject white matter atlas with comprehensive white matter parcellation. ## MNI coordinate: 181 x 217 x 181 (1 mm isotropic) ## Talairach coordinate: 181 x 217 x 181 (1 mm isotropic) # Group-averaged atlases: This atlas was created from their normal DTI database (n = 28). The template was MNI-ICBM-152 and the data from the normal subjects were normalized by affine transformation. Image dimensions are 181x217x181, 1 mm isotropic. There are two types of maps. The first one is the averaged tensor map and the second one is probabilistic maps of 11 white matter tracts reconstructed by FACT. # ICBM Group-averaged atlases: This atlas was created from ICBM database. All templates follow Radiology convention. You may need to flip right and left when you use image registration software that follows the Neurology convention.

Proper citation: DTI White Matter Atlas (RRID:SCR_005279) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.oxfordjournals.org/content/early/2012/05/10/bioinformatics.bts271.full.pdf

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 7,2024. Software for somatic single nucleotide variant (SNV) and small indel detection from sequencing data of matched tumor-normal samples. The method employs a novel Bayesian approach which represents continuous allele frequencies for both tumor and normal samples, whilst leveraging the expected genotype structure of the normal. This is achieved by representing the normal sample as a mixture of germline variation with noise, and representing the tumor sample as a mixture of the normal sample with somatic variation. A natural consequence of the model structure is that sensitivity can be maintained at high tumor impurity without requiring purity estimates. The method has superior accuracy and sensitivity on impure samples compared to approaches based on either diploid genotype likelihoods or general allele-frequency tests.

Proper citation: Strelka (RRID:SCR_005109) Copy   

•   Source: SciCrunch Registry

http://biobankireland.com/

Biobank Ireland Trust promotes the development of an Irish Hospital Biobank Network to coordinate collection of small samples of cancer and normal tissue and coded patient data from those having a cancer operation. This will facilitate international molecular research collaborations, which may help identify the best treatment for each individual patient - personalized medicine. Biobank Ireland is promoting the development of a Hospital Biobank Network throughout the island of Ireland as a bridge between cancer research and care. This new infrastructure will facilitate large national and international translational research collaborations that will raise Ireland''s research profile and benefit those with cancer. Researchers will have online access to samples and to restricted patient data from participating hospitals and an equitable withdrawal process for scientifically and ethically approved projects. Important research results will be explained to the public. Other Objectives: * To facilitate (inter)national translational research collaborations that may lead to new tests and better, less toxic treatments for those with cancer * To enable molecular research on cancer tissue from clinical trials patients identify the best treatment for each individual patient ������??personalized medicine������?? * Researchers will have online access to samples and restricted patient data from participating hospitals, and a fair release process for scientifically and ethically approved projects * Biobank Ireland recognizes the need to have harmonization in biobanking around the world * Important research results will be explained to the public * Biobank Ireland will seek to have the hospital-based Biobank Network funded by government as standard of care

Proper citation: Biobank Ireland Trust (RRID:SCR_006430) Copy   

•   Source: SciCrunch Registry

http://www.wriwindber.org/wriwindber/Platforms/TissueBanking.aspx

Under the direction of Stella Somiari, Ph.D., the tissue bank at Windber Research Institute acquires and banks large numbers of high quality and well annotated normal and diseased tissue specimens. These specimens are obtained from fully informed and consented donors using Institutional Review Board (IRB) approved protocols and are accompanied by detailed clinical, family history and demographic information. The tissue bank has established Standard Operating Procedures (SOPs) for tissue acquisition, handling, processing, packaging and shipping. All collaborators at participating clinics/medical centers utilize these procedures to ensure that the integrity of the specimen is maintained. Tissue types in our collection include plasma, serum, tissue embedded in optimum cutting temperature (OCT), formalin fixed paraffin embedded, and flash frozen. We also isolate and bank tissue derived products such as DNA, RNA and protein for research. Very stringent SOPs are in place for the process of extraction of these tissue-derived products and for quality control/quality assurance (QA/QC). The WRI tissue bank currently has 5 isothermal freezers each with the capacity to store 36,000 specimens. For all specimens obtained from surgical procedures, routine histology is performed to obtain representative Hematoxylin and Eosin (H & E) stained sections for imaging/archiving. All H & E sections are imaged on the Trestle SL-50 imaging system and these images are available online to designated collaborative sites. A certified pathologist verifies all tissue specimens and WRI has telepathology capabilities, which can also be utilized for pathology verification when a second pathologist opinion is required to confirm specimen diagnosis. Other uses of the telepathology capabilities include the verification of Laser Capture Microdissection (LCM) sections (by pathologist) to ensure the correct areas are captured for research. The telepathology system at WRI is the Trestle Corporation's Medmicro system, which permits the pathologist to remotely view, navigate and share images at sub-micron resolution over standard internet connections in real-time.

Proper citation: Windber Tissue Bank (RRID:SCR_000509) Copy   

•   Source: SciCrunch Registry

http://www.med.umkc.edu/psychiatry/nbtb/

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 31, 2016. The UMKC Neuroscience Brain Tissue Bank and Research Laboratory has been established to obtain, process, and distribute human brain tissue to qualified scientists and clinicians dedicated to neuroscience research. No other living organ approaches the human brain in complexity or capacity. Healthy, it astounds and inspires miracles. Diseased, it confounds and diminishes hope. The use of human brain tissue for research will provide insight into the anatomical and neurochemical aspects of diseased and non-diseased brains. While animal models are helpful and necessary in understanding disease, certain disorders can be more efficiently studied using human brain tissue. Also, modern research techniques are often best applied to human tissue. We also need samples of brain tissue that have not been affected by disease. They help us to compare a 'normal' brain with a diseased one. Also, we have a critical need for brain donations from relatives who have genetically inherited disorders. Tissue preparation consists of fresh quick-frozen tissue blocks or coronal slices (nitrogen vapor frozen; custom dissection of specific anatomic regions) or formalin-fixed coronal slices (custom dissection of specific anatomic regions).

Proper citation: UMKC Neuroscience Brain Tissue Bank and Research Laboratory (RRID:SCR_005148) Copy   

•   Source: SciCrunch Registry

http://www.cvrgrid.org/

Infrastructure for sharing cardiovascular data and data analysis tools. Human ExVivo heart data set and canine ExVivo normal and failing heart data sets are available. Canine hearts atlas and human InVivo atlases are available.

Proper citation: CardioVascular Research Grid (CVRG) (RRID:SCR_004472) Copy   

•   Source: SciCrunch Registry

http://stemcellcommons.org/

Open source environment for sharing, processing and analyzing stem cell data bringing together stem cell data sets with tools for curation, dissemination and analysis. Standardization of the analytical approaches will enable researchers to directly compare and integrate their results with experiments and disease models in the Commons. Key features of the Stem Cell Commons * Contains stem cell related experiments * Includes microarray and Next-Generation Sequencing (NGS) data from human, mouse, rat and zebrafish * Data from multiple cell types and disease models * Carefully curated experimental metadata using controlled vocabularies * Export in the Investigation-Study-Assay tabular format (ISA-Tab) that is used by over 30 organizations worldwide * A community oriented resource with public data sets and freely available code in public code repositories such as GitHub Currently in development * Development of Refinery, a novel analysis platform that links Commons data to the Galaxy analytical engine * ChIP-seq analysis pipeline (additional pipelines in development) * Integration of experimental metadata and data files with Galaxy to guide users to choose workflows, parameters, and data sources Stem Cell Commons is based on open source software and is available for download and development.

Proper citation: Stem Cell Commons (RRID:SCR_004415) Copy   

•   Source: SciCrunch Registry

http://en.wikibooks.org/wiki/MINC/Atlases

A linear average model atlas produced by the International Consortium for Brain Mapping (ICBM) project. A set of full- brain volumetric images from a normative population specifically for the purposes of generating a model were collected by the Montreal Neurological Institute (MNI), UCLA, and University of Texas Health Science Center at San Antonio Research Imaging Center (RIC). 152 new subjects were scanned using T1, T2 and PD sequences using a specific protocol. These images were acquired at a higher resolution than the original average 305 data and exhibit improved contrast due predominately to advances in imaging technology. Each individual was linearly registered to the average 305 and a new model was formed. In total, three models were created at the MNI, the ICBM152_T1, ICBM152_T2 and ICBM152_PD from 152 normal subjects. This resulting model is now known as the ICBM152 (although the model itself has not been published). One advantage of this model is that it exhibits better contrast and better definition of the top of the brain and the bottom of the cerebellum due to the increased coverage during acquisition. The entirely automatic analysis pipeline of this data also included grey/white matter segmentation via spatial priors. The averaged results of these segmentations formed the first MNI parametric maps of grey and white matter. The maps were never made publicly available in isolation but have formed parts of other packages for some time including SPM, FSL AIR and as models of grey matter for EEG source location in VARETTA and BRAINWAVE. Again, as these models are an approximation of Talairach space, there are differences in varying areas, to continue our use of origin shift as an example, the ICBM models are approximately 152: +3.5mm in Z and +-co-ordinate -3.5mm and 2.0mm in Y as compared to the original Talairach origin. In addition to the standard analysis performed on the ICBM data, 64 of the subjects data were segmented using model based segmentation. 64 of the original 305 were manually outlined and a resulting parametric VOI atlas built. The native data from these acquisitions was 256x256 with 1mm slices. The final image resolution of this data was 181x217x181 with 1mm isotropic voxels. Refer to the ICBM152 NonLinear if you are fitting an individual to model and do not care about left/right comparisons. A short history of the various atlases that have been produced at the BIC (McConnell Brain Imaging Center, Montreal Neurological Institute) is provided.

Proper citation: MINC/Atlases (RRID:SCR_005281) Copy   

•   Source: SciCrunch Registry

http://headit.ucsd.edu

Platform for sharing, download, and re-analysis or meta-analysis of sophisticated, fully annotated, human electrophysiological data sets. It uses EEG Study Schema (ESS) files to provide task, data collection, and subject metadata, including Hierarchical Event Descriptor (HED) tag descriptions of all identified experimental events. Visospatial task data also available from, http://sccn.ucsd.edu/eeglab/data/headit.html: A 238-channel, single-subject EEG data set recorded at the Swartz Center, UCSD, by Arnaud Delorme, Julie Onton, and Scott Makeig is al.

Proper citation: HeadIT (RRID:SCR_005657) Copy   

•   Source: SciCrunch Registry