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RUCDR is a biobank and a service organization that maintains human blood, serum, saliva, tissue and the genetic products derived from those. Services include technical consultation and logistical support for biobanking. Researchers can order biomaterials and apply for phenotypic / genotypic data.
Proper citation: Rutgers Cell and DNA Repository (RRID:SCR_010624) Copy
International biobank storing whole blood and DNA from 200,000 individuals, serum and plasma samples from more than 100,000 individuals as well as urine, RNA tubes, cells, buffy coat and Na-heparin tubes for environmental analysis for as many as 50,000 individuals. All bio-specimens from the HUNT surveys are collected, processed and stored at the HUNT Biobank in Levanger. The National CONOR Biobank is located on the same site, where it serves as a central research repository for DNA samples from all the largest Norwegian health surveys. These make up the Cohorts of Norway (CONOR), which include samples from more than 200,000 individuals. * HUNT 1 was carried out in 1984-1986 to establish the health history of 75,000 people. * HUNT 2, carried out in 1995-1997, focused on the evolution of the health history of 74,000 people. This included blood sample collection from 65,000 people. The data that accompany biospecimens in the biobank are stored in secured computer systems that run complex database management and analysis software. * HUNT 3 was completed in June 2008. 93,210 people were invited to participate in the study, and as of the 6th of June, 2008, 48,289 people participated (52% participation rate). The data, collected by means of questionnaires, interviews, clinical examinations and collection of blood and urine samples, will be ready for analysis in January 2009. * Young-HUNT is the adolescent part of HUNT including participants aged 13-19 years. Young-HUNT1 (1995-97) was conducted as part of HUNT2, 9141 adolescents participated (90% response rate). Young-HUNT2 (2000-01) was a follow-up study of Young-HUNT1, 2400 students participated in both studies (77% of the invited). Young-HUNT3 (2006-08) was a new cross-sectional study as part of HUNT3. This time 8677 adolescents participated (87% response rate). Data collection included self-reported questionnaires, structured interviews, clinical measurements and, in Young-HUNT3, buccal smears. All institutions with research expertise can apply for access to analyze HUNT data. Projects must have recommendations from The Regional Committee for Medical Research in Norway (REK) and be registered with The Norwegian Social Science Data Services (NSD).
Proper citation: Hunt Biobank (RRID:SCR_010626) Copy
http://www.mcid.co.uk/Software/MCID_Analysis
Software designed to provide an image analysis software solution for offline analysis of images, ideally for the analysis of images where image capture is not required. Available applications for MCID Analysis include gel/blot analysis, fluorescence microscopy, and stereology.
Proper citation: MCID Analysis (RRID:SCR_014278) Copy
Software used to analyze and quantify images stained with multiple fluorophores in vitro or in vivo. It can output both image and value outputs.
Proper citation: SMIA-CUKIE (RRID:SCR_014795) Copy
http://sourceforge.net/projects/erppcatoolkit/
This Matlab toolkit is a general purpose tool for editing, visualizing, and analyzing EEG data (both Event Related Potential - ERP and spectral) whose most recent version has been downloaded over 1000 times. Its three chief highlights are: 1) an optimized automatic artifact correction function that includes ICA correction for eye blinks and saccades. 2) Extensive support for easily conducting PCA and ICA through all stages of the procedure, including inspection of reconstituted waveforms and batch ANOVAs. 3) Implementation of robust ANOVAs, including McCarthy-Wood vector test. It has a graphical user interface for point and click usage and comes with an extensive illustrated tutorial. A description of the toolkit was published in Dien (2010) in Journal of Neuroscience Methods. It relies on both internal functions as well as borrowed functions from both EEGlab and FieldTrip.
Proper citation: ERP PCA Toolkit (RRID:SCR_013105) Copy
The NCBCs are a set of networked computation core facilities for biomedical infrastructure funded under the NIH Common Fund, the National Program of Excellence in Biomedical Computing (NPEBC). There are seven funded Centers that cover systems biology, image processing, biophysical modeling, biomedical ontologies, information integration, and tools for gene-phenotype and disease analysis. The centers will create innovative software programs and other tools that enable the biomedical community to integrate, analyze, model, simulate, and share data on human health and disease. Each Center has Cores that are focused on (1) computational science, (2) biomedical computational science and (3) driving biological projects whose intent is to drive the interaction between computational and biomedical computational science. In addition to the Centers, the NIH has a number of active program announcements to develop collaborations with the biomedical research community��this includes announcements from the Biomedical Information Science and Technology Initiative (BISTI) and the Program for Collaborations with National Centers for Biomedical Computing. There are numerous efforts in education and training that emanate from the Centers and there is an annual all hands meeting.
Proper citation: National Centers for Biomedical Computing (RRID:SCR_010635) Copy
http://www.nitrc.org/projects/shapepopviewer/
Software that allows users to dynamically interact with multiple surfaces simultaneously. It is very useful for visualisation and comparison of 3D surfaces by also displaying their scalars or vectors attributes stored in the points, and allowing the user to simply modify the colormap. ShapePopulationViewer is available as an extension of 3D Slicer.
Proper citation: ShapePopulationViewer (RRID:SCR_014167) Copy
Joint Information Systems Committee (JISC) is the UK''s expert on information and digital technologies for education and research. JISC inspires UK colleges and universities in the innovative use of digital technologies, helping to maintain the UK''s position as a global leader in education. JISC helps institutions make best use of technology to manage all aspects of their business. JISC provides access to the world-class Janet (UK) network, quality digital resources and a range of specialist advisory services. JISC provides: * A world-class network - JANET * Access to electronic resources * New environments for learning, teaching and research * Guidance on institutional change * Advisory and consultancy services * Regional support - JISC RSCs Partnerships JISC develops partnerships to enable the UK education and research communities to engage in national and global collaborations to overcome the challenges of delivering world-class ICT solutions and services. Funding Opportunities JISC funds a wide range of infrastructure, services, innovative projects and studies. A large number of these originate from a successful response to a grant funding call (previously known as a JISC Circular), inviting eligible HE and FE institutions to bid for project funding. JISC also procures other activities (usually studies such as an evaluation or market research), through invitations to tender which are available to other organizations to bid against. JISC is the name of our organization. Historically, it stood for Joint Information Systems Committee.
Proper citation: JISC (RRID:SCR_011331) Copy
http://alan-hadley.software.informer.com/
A software used to process stacks of digital images. All of the resulting images are processed to have the same dimensions and then are consolidated into a single image.
Proper citation: CombineZP (RRID:SCR_014567) Copy
A nanoparticle research collaborative which engineers nanoparticle products in order to find cures for cancer and other diseases. The gold labels produced are uncharged molecules which are cross-linked to specific sites on biomolecules. Labels can be attached to any molecule with a reactive group (proteins, peptides, oligonucleotides, small molecules and lipids) for detection and localization. New probes can be engineered based on any fragment of a naturally occurring biomolecule, and the label can be positioned away from the binding site so it does not interfere with binding.
Proper citation: nanoprobes.com (RRID:SCR_014323) Copy
A data center that develops evaluated mass spectral libraries and provides related software tools that assist compound identification by providing reference mass spectra for GC/MS (by electron ionization) and LC-MS/MS (by tandem mass spectrometry). It also provides gas phase retention indices for GC. Resources include the mass spectral library, the peptide library, and a standard refernece material guide.
Proper citation: NIST Mass Spectrometry Data Center (RRID:SCR_014680) Copy
https://github.com/Brazelton-Lab/seq-annot
Software Python package for annotating and counting genomic features in genomes and metagenomes. Software tools to facilitate annotation and comparison of genomes and metagenomes.
Proper citation: seq-annot (RRID:SCR_018731) Copy
https://usa.jpk.com/news/2011/directoverlay-display-analysis-software-from-jpk-instruments
Software package for display of light microscopy images together with atomic force microscopy images.
Proper citation: DirectOverlay (RRID:SCR_018978) Copy
Software tool as a unified analytics engine for large scale data processing. An open source distributed general purpose cluster computing framework.
Proper citation: Apache Spark (RRID:SCR_016557) Copy
http://regent.qc.ca/assets/winrhizo_software.html
Software toolbox for image analysis by Regent Instruments Inc. Used for root measurement in different forms like morphology, topology, architecture and color analyses. Automatically or interactively analyses washed roots.
Proper citation: WinRHIZO (RRID:SCR_017120) Copy
https://www.globalphasing.com/autoproc/
Data processing software for X-ray diffraction data. autoPROC is a set of tools and programs to automate steps involved in data processing, such as image analysis, integration, indexing, and determination.
Proper citation: autoPROC (RRID:SCR_015748) Copy
Commerciall organization to develop study protocols collaboratively to run and manage animal research studies for academic, government, biotech and pharmaceutical labs. Provides services, including product installation and configuration, user training, customization services and ongoing support.
Proper citation: Studylog (RRID:SCR_016682) Copy
https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005095
Software tool to describe spatial patterns in degrees of inhomogeneity and to incorporate intensity based correction to analyze images with wide range of resolutions. Can be used to assess protein and lipid patterns, quantifying distribution changes and spatial reorganization at cell surface.
Proper citation: QuASIMoDOH (RRID:SCR_018708) Copy
Benchtop genetic analyzer. Electrophoresis system for DNA and RNA sample quality control. It can be used for next generation sequencing or Biobank workflow.
Proper citation: Agilent: 4200 TapeStation System (RRID:SCR_018435) Copy
https://github.com/zhengkaiyu/FIMAS
Software tool to perform basic and specific analysis procedures on fluorescent microscopy and fluorescent lifetime imaging microscopy data. Requires MATLAB with image processing and statistical toolboxes. Can import fluorescent data from Olympus, Biorad, Femtonics, TIFF, Excel, ASCII files.
Proper citation: Fluorescent Imaging Analysis Software FIMAS (RRID:SCR_018311) Copy
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