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The MiND: Metadata in NIfTI for DWI framework enables data sharing and software interoperability for diffusion-weighted MRI. This site provides specification details, tools, and examples of the MiND mechanism for representing important metadata for DWI data sets at various stages of post-processing. MiND framework provides a practical solution to the problem of interoperability between DWI analysis tools, and it effectively expands the analysis options available to end users. To assist both users and developers in working with MiND-formatted files, we provide a number of software tools for download. * MiNDHeader A utility for inspecting MiND-extended files. * I/O Libraries Programming libraries to simplify writing and parsing MiND-formatted data. * Sample Files Example files for each MiND schema. * DIRAC LONI''s Diffusion Imaging Reconstruction and Analysis Collection is a DWI processing suite which utilizes the MiND framework.
Proper citation: LONI MiND (RRID:SCR_004820) Copy
http://www.sph.umich.edu/csg/abecasis/CaTS
Software tool for carrying out power calculations for large genetic association studies, including two stage genome wide association studies.
Proper citation: Calculator for Association with Two Stage design (RRID:SCR_007238) Copy
http://immport.org/immport-open/public/reference/cytokineRegistry
A registry of cytokines, chemokines, and receptors generated for the purpose of collecting, integrating, and mapping between entity names and synonyms from several resources. These resources include MeSH, the Protein Ontology, EntrezGene, HGNC, MGI, UniProt and others.
Proper citation: Cytokine Registry (RRID:SCR_014368) Copy
https://bioinformatics.niaid.nih.gov/chemokinedb/
Resource of chemokines and receptors with detailed information including taxonomy, nomenclature, structure, physiological function, tissue information, and phenotype, collected from IUPHAR/BPS, UniGene, and UniProt public databases.
Proper citation: ChemokineDB (RRID:SCR_016593) Copy
http://software.broadinstitute.org/gsea/msigdb/index.jsp
Collection of annotated gene sets for use with Gene Set Enrichment Analysis (GSEA) software.
Proper citation: Molecular Signatures Database (RRID:SCR_016863) Copy
https://github.com/VH-Lab/vhlab-microscopyimageanalysis-matlab
Software Matlab app for analysis of high density imaging data like that from Array Tomography.
Proper citation: vhlab-microscopyimageanalysis-matlab (RRID:SCR_024450) Copy
A commercial supplier of custom synthetic molecules. They specialize in peptides, oligonucleotides, bioconjugation, molecular biology services, proteins and specialty chemistry.
Proper citation: Bio-Synthesis (RRID:SCR_000820) Copy
https://github.com/YuanXue1993/SegAN
Image analysis software for medical image segmentation. The software is fueled by an end-to-end adversarial neural network that generates segmentation label maps.
Proper citation: SegAN (RRID:SCR_016215) Copy
Project to create complete mesoscale connectivity atlas of the C57Black/6 mouse brain and to subsequently generate its global neural networks.
Proper citation: Mouse Connectome Project (RRID:SCR_017313) Copy
Nonhuman Primate reference transcriptome resource consisting of deep sequencing complete transcriptomes (RNA-seq) from multiple NHP species.
Proper citation: Nonhuman Primate Reference Transcriptome Resource (RRID:SCR_017534) Copy
http://www.sb.fsu.edu/~rsref/Distribution/roadmap_distribution.htm
Software tool to display surface of macromolecule and its properties. Uses projections to map van der Waals or solvent accessible surface of macromolecule onto plane., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Roadmap (RRID:SCR_017207) Copy
http://compbio.cs.princeton.edu/conservation/
Software for scoring protein sequence conservation using the Jensen-Shannon divergence. It can be used to predict catalytic sites and residues near bound ligands.
Proper citation: Conservation (RRID:SCR_016064) Copy
Software tool for genome and metagenome distance estimation using MinHash. Reduces large sequences and sequence sets to small, representative sketches, from which global mutation distances can be rapidly estimated.
Proper citation: Mash (RRID:SCR_019135) Copy
http://ki-su-arc.se/dementia-in-swedish-twins-harmony/
A twin study characterizing the importance of genetic factors for dementia and using discordant twin pairs to study other putative risk factors which control for genetic propensity to develop the disease. Molecular genetic studies have identified a number of mutations and other markers associated with early age of onset Alzheimer''''s disease. However, most cases of late age of onset dementia are considered sporadic, that is, without a clear genetic basis. Twin studies provide a unique opportunity to characterize the importance of genetic factors for dementia. Discordant twin pairs additionally provide the opportunity to study other putative risk factors which controlling for genetic propensity to develop the disease. In the first wave of the Study of Dementia in Swedish Twins, all SATSA twins born before 1935 have been screened for dementia symptoms. Over 190 suspects have been identified. This pilot study has been expanded to the entire registry in the study known as HARMONY. All twins aged 65 and older were invited to participate in a computer assisted telephone screening interview. A total of 13,519 individuals completed the interview (response rate = 75.9%). Dementia screening was based on the TELE, which includes the 10-item MSQ, other cognitive items (counting backwards, recalling three words, and similarities), and questions about health and daily functioning; or on Blessed scores obtained from a proxy interview. Among those screened, 1565 were positive for suspicion of dementia and were referred for complete clinical evaluation by a physician and a nurse. Once the preliminary in-person evaluation suggested that the suspected case was demented, the twin partner was also invited for an identical clinical work-up. Response rate for clinical evaluations is 71.4%. Approximately half of those visited for evaluation have been diagnosed as demented according to DSM-IV criteria, of which two-thirds have Alzheimer''''s disease. An extensive assessment of probable risk exposure is also included. Longitudinal follow-up is yet another feature of the study. Association studies with candidate genes are also being performed. Types of samples * DNA Number of sample donors * 1154 (sample collection completed)
Proper citation: KI Biobank - HARMONY (RRID:SCR_008884) Copy
Website for brain experimental data and other resources such as stimuli and analysis tools. Provides marketplace and discussion forum for sharing tools and data in neuroscience. Data repository and collaborative tool that supports integration of theoretical and experimental neuroscience through collaborative research projects. CRCNS offers funding for new class of proposals focused on data sharing and other resources.
Proper citation: CRCNS (RRID:SCR_005608) Copy
A web portal that provides access to data, tools and materials that will aid in craniofacial research. Included is access to genomic and imaging based data sets from a variety of species, including zebrafish, human and mouse.
Proper citation: FaceBase (RRID:SCR_005998) Copy
http://www.ncbi.nlm.nih.gov/pubmedcommons/
A forum where authors who have published in PubMed may comment on any publication in PubMed. Members of PubMed Commons are not anonymous and must agree to certain terms and guidelines concerning appropriate and inapproriate comments.
Proper citation: Pubmed Commons (RRID:SCR_014021) Copy
https://metagenote.niaid.nih.gov/
Quick and intuitive way to annotate data from genomics studies including microbiome. Project to aid researchers in applying standardized metadata describing what, where, how, and when of samples collected in genomics study. Collection of METAdata of GEnomics studies on web based NOTEbook. Metadata are stored in centralized repository and validated according to guidelines from Genomics Standard Consortium, which are also supported by repositories and large microbiome initiatives such as NCBI, European Bioinformatics Institute (EBI), and Earth Microbiome Project. Upon request from researchers, data will also be submitted for publication via NCBI Sequence Read Archive (SRA) repository.
Proper citation: METAGENOTE (RRID:SCR_018494) Copy
http://www.project-redcap.org/
Web application that allows users to build and manage online surveys and databases. Using REDCap's stream-lined process for rapidly developing projects, you may create and design projects using 1) the online method from your web browser using the Online Designer; and/or 2) the offline method by constructing a "data dictionary" template file in Microsoft Excel, which can be later uploaded into REDCap. Both surveys and databases (or a mixture of the two) can be built using these methods. REDCap provides audit trails for tracking data manipulation and user activity, as well as automated export procedures for seamless data downloads to Excel, PDF, and common statistical packages (SPSS, SAS, Stata, R). Also included are a built-in project calendar, a scheduling module, ad hoc reporting tools, and advanced features, such as branching logic, file uploading, and calculated fields. REDCap has a quick and easy software installation process, so that you can get REDCap running and fully functional in a matter of minutes. Several language translations have already been compiled for REDCap (e.g. Chinese, French, German, Portuguese), and it is anticipated that other languages will be available in full versions of REDCap soon. The REDCap Shared Library is a repository for REDCap data collection instruments and forms that can be downloaded and used by researchers at REDCap partner institutions.
Proper citation: REDCap (RRID:SCR_003445) Copy
Web based collaborative text annotation tool. Used for managing multi-user, multi-label document annotation. Project managers can specify annotation schema for entities and relations and select annotators and distribute documents anonymously to prevent bias. Document input format can be plain text, PDF or BioC (uploaded locally or automatically retrieved from PubMed/PMC), and output format is BioC with inline annotations. Displays figures from full text.
Proper citation: TeamTat (RRID:SCR_023439) Copy
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