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http://s-quest.bihealth.org/fiddle/

Software interactive tool to help researchers to identify most appropriate publication format for their dataset that may be hard to publish in traditional journals. Formats include data repositories, micropublications, preprints, data journals, publishing platforms and journals that are open to null results. Users can search for publication format that meets their needs, compare and contrast formats, and find links to publishers. Open source tool to combat publication bias by getting research out of file drawer and into scientific community.

Proper citation: fiddle (RRID:SCR_017327) Copy   

•   Source: SciCrunch Registry
  

http://www.cancerimagingarchive.net/

Archive of medical images of cancer accessible for public download. All images are stored in DICOM file format and organized as Collections, typically patients related by common disease (e.g. lung cancer), image modality (MRI, CT, etc) or research focus. Neuroimaging data sets include clinical outcomes, pathology, and genomics in addition to DICOM images. Submitting Data Proposals are welcomed.

Proper citation: Cancer Imaging Archive (TCIA) (RRID:SCR_008927) Copy   

•   Source: SciCrunch Registry
  

http://jcb-dataviewer.rupress.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. A web-based, multi-dimensional image data-viewing application for original microscopy image datasets associated with articles published in The Journal of Cell Biology, a peer-reviewed journal published by The Rockefeller University Press. The JCB DataViewer can host multidimensional fluorescence microscopy images, 3D tomogram data, very large (gigapixel) images, and high content imaging screens. Images are presented in an interactive viewer, and the scores from high content screens are presented in interactive graphs with data points linked to the relevant images. The JCB DataViewer uses the Bio-Formats library to read over 120 different imaging file formats and convert them to the OME-TIFF image data standard. Image data are archived by the Journal and may be freely accessed by readers using the JCB DataViewer. Download of author-provided image data and associated metadata in OME-TIFF format is also possible with author permission, allowing for independent analysis of image data irrespective of acquisition or viewing software. Although the JCB DataViewer is designed to host and facilitate sharing and analysis of original microscopy image data, authors may also upload other types of original image data as supplements to their manuscripts, including histology and electron micrographs and digital scans of gels or blots.

Proper citation: JCB DataViewer (RRID:SCR_002633) Copy   

•   Source: SciCrunch Registry
  

https://www.qut.edu.au/research/research-projects/landmark-biobanks

A repository of human tissue samples collected during the LANDMark study (Longitudinal Assessment of Neuropathy in Diabetes using novel ophthalmic markers). The LANDMark Biobank longitudinal dataset contains blood and tissue (skin) samples and matching detailed phenotypic data of three microvascluar complications of type 1 diabetes: neuropathy, nephropathy and retinopathy.

Proper citation: LANDMark BioBanks (RRID:SCR_014534) Copy   

•   Source: SciCrunch Registry
  

http://brainmaps.org

An interactive multiresolution brain atlas that is based on over 20 million megapixels of sub-micron resolution, annotated, scanned images of serial sections of both primate and non-primate brains and integrated with a high-speed database for querying and retrieving data about brain structure and function. Currently featured are complete brain atlas datasets for various species, including Macaca mulatta, Chlorocebus aethiops, Felis catus, Mus musculus, Rattus norvegicus, Tyto alba and many other vertebrates. BrainMaps is currently accepting histochemical, immunocytochemical, and tracer connectivity data, preferably whole-brain. In addition, they are interested in EM, MRI, and DTI data.

Proper citation: BrainMaps.org (RRID:SCR_006878) Copy   

•   Source: SciCrunch Registry
  

https://scicrunch.org/ResourceWatch

Knowledgebase of biomedical research resources. Repository for storing validation and problematic information about variety of entities within biomedical domain, such as antibodies, cell lines, etc. Enables researchers to submit their own claims about specific entity to make validation/problematic information F.A.I.R. (Findable, Accessable, Interoperable, Reuseable).

Proper citation: Biomed Resource Watch (RRID:SCR_021761) Copy   

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http://www.ncbi.nlm.nih.gov/pmc/

Collection of full text archive of biomedical and life sciences journal literature at U.S. National Institutes of Health National Library of Medicine (NIH/NLM). With PubMed Central, NCBI is taking lead in preserving and maintaining open access to electronic literature. Value of PubMed Central, in addition to its role as an archive, lies in what can be done when data from diverse sources is stored in common format in single repository. All articles in PMC are free (sometimes on a delayed basis). Some journals go beyond free, to Open Access.

Proper citation: PubMed Central (RRID:SCR_004166) Copy   

•   Source: SciCrunch Registry
  

http://www.emdataresource.org/

Portal for deposition and retrieval of cryo electron microscopy (3DEM) density maps, atomic models, and associated metadata. Global resource for 3 Dimensional Electron Microscopy structure data archiving and retrieval, news, events, software tools, data standards, validation methods.

Proper citation: EMDataResource.org (RRID:SCR_003207) Copy   

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http://bioinfo2.ugr.es/NGSmethDB/

A dedicated database for the storage, browsing and data mining of whole-genome, single-base-pair resolution methylomes.

Proper citation: NGSmethDB (RRID:SCR_012847) Copy   

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http://www.genesigdb.org

Database of traceable, standardized, annotated gene signatures which have been manually curated from publications that are indexed in PubMed. The Advanced Gene Search will perform a One-tailed Fisher Exact Test (which is equivalent to Hypergeometric Distribution) to test if your gene list is over-represented in any gene signature in GeneSigDB. Gene expression studies typically result in a list of genes (gene signature) which reflect the many biological pathways that are concurrently active. We have created a Gene Signature Data Base (GeneSigDB) of published gene expression signatures or gene sets which we have manually extracted from published literature. GeneSigDB was creating following a thorough search of PubMed using defined set of cancer gene signature search terms. We would be delighted to accept or update your gene signature. Please fill out the form as best you can. We will contact you when we get it and will be happy to work with you to ensure we accurately report your signature. GeneSigDB is capable of providing its functionality through a Java RESTful web service.

Proper citation: GeneSigDB (RRID:SCR_013275) Copy   

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https://omictools.com/l2l-tool

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 26, 2019.

Database of published microarray gene expression data, and a software tool for comparing that published data to a user''''s own microarray results. It is very simple to use - all you need is a web browser and a list of the probes that went up or down in your experiment. If you find L2L useful please consider contributing your published data to the L2L Microarray Database in the form of list files. L2L finds true biological patterns in gene expression data by systematically comparing your own list of genes to lists of genes that have been experimentally determined to be co-expressed in response to a particular stimulus - in other words, published lists of microarray results. The patterns it finds can point to the underlying disease process or affected molecular function that actually generated the observed changed in gene expression. Its insights are far more systematic than critical gene analyses, and more biologically relevant than pure Gene Ontology-based analyses. The publications included in the L2L MDB initially reflected topics thought to be related to Cockayne syndrome: aging, cancer, and DNA damage. Since then, the scope of the publications included has expanded considerably, to include chromatin structure, immune and inflammatory mediators, the hypoxic response, adipogenesis, growth factors, hormones, cell cycle regulators, and others. Despite the parochial origins of the database, the wide range of topics covered will make L2L of general interest to any investigator using microarrays to study human biology. In addition to the L2L Microarray Database, L2L contains three sets of lists derived from Gene Ontology categories: Biological Process, Cellular Component, and Molecular Function. As with the L2L MDB, each GO sub-category is represented by a text file that contains annotation information and a list of the HUGO symbols of the genes assigned to that sub-category or any of its descendants. You don''''t need to download L2L to use it to analyze your microarray data. There is an easy-to-use web-based analysis tool, and you have the option of downloading your results so you can view them at any time on your own computer, using any web browser. However, if you prefer, the entire L2L project, and all of its components, can be downloaded from the download page. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: L2L Microarray Analysis Tool (RRID:SCR_013440) Copy   

•   Source: SciCrunch Registry
  

https://inrae.github.io/ODAM/

Software experimental data table management system to make research data accessible and available for reuse with minimal effort on part of data provider. Allows any scientist or data researcher to be able to explore dataset and then extract some or all of data according to their needs. Designed to manage experimental data tables in quick and easy way for users.

Proper citation: ODAM (RRID:SCR_018774) Copy   

•   Source: SciCrunch Registry
  

https://github.com/INCF/swc-specification

Software repository contains files needed to build the standard and its supplementary documentation. Changes are automatically pushed and built. Information about the SWC file specification.

Proper citation: SWC format (RRID:SCR_027631) Copy   

•   Source: SciCrunch Registry
  

http://crcview.hegroup.org/

Web-based microarray data analysis and visualization system powered by CRC, or Chinese Restaurant cluster, a Dirichlet process model-based clustering algorithm recently developed by Dr. Steve Qin. It also incorporates several gene expression analysis programs from Bioconductor, including GOStats, genefilter, and Heatplus. CRCView also installs from the Bioconductor system 78 annotation libraries of microarray chips for human (31), mouse (24), rat (14), zebrafish (1), chicken (1), Drosophila (3), Arabidopsis (2), Caenorhabditis elegans (1), and Xenopus Laevis (1). CRCView allows flexible input data format, automated model-based CRC clustering analysis, rich graphical illustration, and integrated Gene Ontology (GO)-based gene enrichment for efficient annotation and interpretation of clustering results. CRC has the following features comparing to other clustering tools: 1) able to infer number of clusters, 2) able to cluster genes displaying time-shifted and/or inverted correlations, 3) able to tolerate missing genotype data and 4) provide confidence measure for clusters generated. You need to register for an account in the system to store your data and analyses. The data and results can be visited again anytime you log in.

Proper citation: CRCView (RRID:SCR_007092) Copy   

•   Source: SciCrunch Registry
  

https://www.hmpdacc.org/ihmp/

Provides human microbiome datasets and minimum reporting standards established by DCC, from both initial HMP-1 phase and iHMP. Offers to query and retrieve metagenomic, metatranscriptomic, human genetic, microbial culture, and many other data types from each project. Provides integrated longitudinal datasets from both microbiome and host from different cohort studies of microbiome associated conditions.

Proper citation: Integrative Human Microbiome Project (RRID:SCR_015586) Copy   

•   Source: SciCrunch Registry
  

http://www.liberatingresearch.org

A repository which hosts and archives original and edited scientific papers. Scientists can post their academic manuscripts on Libre, where they can find reviewers who will formally evaluate the manuscripts. Evaluated works are posted alongside the original manuscript with reviewers' identities disclosed and the work they edit given its own DOI. Users can post additional updated versions of their work to Libre or send their papers to journals. Papers and reviews are rated by other scientists, and from these Libre creates holistic indeces listing the best rated writers and reviewers.

Proper citation: Libre (RRID:SCR_014018) Copy   

•   Source: SciCrunch Registry
  

https://mybinder.org/

Open-source web application for managing digital repositories. Allows to create custom computing environments that can be shared and used by many remote users.Turns a GitHub repository containing a collection of Jupyter Notebooks into a collection of interactive notebooks. With Binder, open those notebooks in an executable environment, making your code immediately reproducible by anyone, anywhere.

Proper citation: Binder (RRID:SCR_016437) Copy   

•   Source: SciCrunch Registry
  

http://www.epilepsygenes.org/page/show/homepage

The Epilepsy Genetic Association Database (epiGAD) is an online repository of data relating to genetic association studies in the field of epilepsy. It summarizes the results of both published and unpublished studies, and is intended as a tool for researchers in the field to keep abreast of recent studies, providing a bird''s eye view of this research area. The goal of epiGAD is to collate all association studies in epilepsy in order to help researchers in this area identify all the available gene-disease associations. Finally, by including unpublished studies, it hopes to reduce the problem of publication bias and provide more accurate data for future meta-analyses. It is also hoped that epiGAD will foster collaboration between the different epilepsy genetics groups around the world, and faciliate formation of a network of investigators in epilepsy genetics. There are 4 databases within epiGAD: - the susceptibility genes database - the epilepsy pharmacogenetics database - the meta-analysis database - the genome-wide association studies (GWAS) database The susceptibility genes database compiles all studies related to putative epilepsy susceptibility genes (eg. interleukin-1-beta in TLE), while the pharmacogenetics studies in epilepsy (eg. ABCB1 studies) are stored in ''phamacogenetics''. The meta-analysis database compiles all existing published epilepsy genetic meta-analyses, whether for susceptibility genes, or pharmacogenetics. The GWAS database is currently empty, but will be filled once GWAS are published. Sponsors: The epiGAD website is supported by the ILAE Genetics Commission.

Proper citation: Epilepsy Genetic Association Database (RRID:SCR_006840) Copy   

•   Source: SciCrunch Registry
  

http://grouthbio.com/Home_Page.html

A comprehensive listing of companies and organizations involved with genomics and molecular biology. There are lists for genome software and services, genome institutions and supplies, and general institutions.

Proper citation: Geoffs Bio-Directories (RRID:SCR_001016) Copy   

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https://web.expasy.org/abcd/

Repository of sequenced antibodies, integrating curated information about antibody and its antigen with cross links to standardized databases of chemical and protein entities. Manually curated repository of sequenced antibodies, developed by Geneva Antibody Facility at University of Geneva, in collaboration with CALIPHO and Swiss Prot groups at SIB Swiss Institute of Bioinformatics. Database provides list of sequenced antibodies with their known targets. Each antibody is assigned unique ID number that can be used in academic publications to increase reproducibility of experiments.

Proper citation: ExPASy ABCD database (RRID:SCR_017401) Copy   

•   Source: SciCrunch Registry