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https://app.terra.bio/#workspaces/pathogen-genomic-surveillance/COVID-19

Broad Terra cloud workspace for best practices with COVID-19 genomics data. Raw COVID-19 sequencing data from NCBI Sequence Read Archive. Workflows for genome assembly, quality control, metagenomic classification, and aggregate statistics.

Proper citation: Broad Terra cloud commons for pathogen surveillance (RRID:SCR_018278) Copy   

•   Source: SciCrunch Registry

http://www.icpsr.umich.edu/SAMHDA/

Database of the nation''s substance abuse and mental health research data providing public use data files, file documentation, and access to restricted-use data files to support a better understanding of this critical area of public health. The goal is to increase the use of the data to most accurately understand and assess substance abuse and mental health problems and the impact of related treatment systems. The data include the U.S. general and special populations, annual series, and designs that produce nationally representative estimates. Some of the data acquired and archived have never before been publicly distributed. Each collection includes survey instruments (when provided), a bibliography of related literature, and related Web site links. All data may be downloaded free of charge in SPSS, SAS, STATA, and ASCII formats and most studies are available for use with the online data analysis system. This system allows users to conduct analyses ranging from cross-tabulation to regression without downloading data or relying on other software. Another feature, Quick Tables, provides the ability to select variables from drop down menus to produce cross-tabulations and graphs that may be customized and cut and pasted into documents. Documentation files, such as codebooks and questionnaires, can be downloaded and viewed online.

Proper citation: Substance Abuse and Mental Health Data Archive (RRID:SCR_007002) Copy   

•   Source: SciCrunch Registry

https://www.bi.mpg.de/borst

Merger of the Max Planck Institute of Neurobiology and the Max Planck Institute of Ornithology and has been renamed to Circuits - Computation – Models. Department devoted to the study of how the brain computes to understand neural information processing at the level of individual neurons and small neural circuits.

Proper citation: Max Planck Institute for Biological Intelligence Circuits - Computation – Models (RRID:SCR_008048) Copy   

•   Source: SciCrunch Registry

http://pepr.cnmcresearch.org/

An experiment in web-database access to large multi-dimensional data sets using a standardized experimental platform to determine if the larger scientific community can be given simple, intuitive, and user-friendly web-based access to large microarray data sets. All data in PEPR is also available via NCBI GEO. The structure and goals of PEPR differ from other mRNA expression profiling databases in a number of important ways. * The experimental platform in PEPR is standardized, and is an Affymetrix - only database. All microarrays available in the PEPR web database should ascribe to quality control and standard operating procedures. A recent publication has described the QC/SOP criteria utilized in PEPR profiles ( The Tumor Analysis Best Practices Working Group 2004 ). * PEPR permits gene-based queries of large Affymetrix array data sets without any specialized software. For example, a number of large time series projects are available within PEPR, containing 40-60 microarrays, yet these can be simply queried via a dynamic web interface with no prior knowledge of microarray data analysis. * Projects in PEPR originate from scientists world-wide, but all data has been generated by the Research Center for Genetic Medicine, Children''''s National Medical Center, Washington DC. Future developments of PEPR will allow remote entry of Affymetrix data ascribing to the same QC/SOP protocols. They have previously described an initial implementation of PEPR, and a dynamic web-queried time series graphical interface ( Chen et al. 2004 ). A publication showing the utility of PEPR for pharmacodynamic data has recently been published ( Almon et al. 2003 ).

Proper citation: Public Expression Profiling Resource (RRID:SCR_007274) Copy   

•   Source: SciCrunch Registry

http://pbil.univ-lyon1.fr/acuts/ACUTS.html

THIS RESOURCE IS NO LONGER IN SERVICE, Documented on August 12, 2014. Database that identifies new regulatory elements in untranslated regions of protein-coding genes (5 prime flanks, 5 prime UTRs, introns, 3 prime UTRs and 3 prime flanks). The analyses is focused on genes from metazoan species (essentially vertebrates, insects and nematodes). Information on highly conserved regions (sequences, alignments, annotations, bibliographic references) are compiled. Currently 176 out of 326 detected highly conserved regions (HCRs) have been analyzed and incorporated in the database. You can also access the list of annotated conserved elements and the list of conserved elements that remain to be processed. Their approach is based on comparative sequence analysis, for the identification of phylogenetic footprints.

Proper citation: Ancient conserved untranslated sequences (RRID:SCR_008130) Copy   

•   Source: SciCrunch Registry

http://bioinfo-out.curie.fr/ittaca/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on 6/12/25. ITTACA is a database created for Integrated Tumor Transcriptome Array and Clinical data Analysis. ITTACA centralizes public datasets containing both gene expression and clinical data and currently focuses on the types of cancer that are of particular interest to the Institut Curie: breast carcinoma, bladder carcinoma, and uveal melanoma. ITTACA is developed by the Institut Curie Bioinformatics group and the Molecular Oncology group of UMR144 CNRS/Institut Curie. A web interface allows users to carry out different class comparison analyses, including comparison of expression distribution profiles, tests for differential expression, patient survival analyses, and users can define their own patient groups according to clinical data or gene expression levels. The different functionalities implemented in ITTACA are: - To test if one or more gene, of your choice, is differentially expressed between two groups of samples exhibiting distinct phenotypes (Student and Wilcoxon tests). - The detection of genes differentially expressed (Significance Analysis of Microarrays) between two groups of samples. - The creation of histograms which represent the expression level according to a clinical parameter for each sample. - The computation of Kaplan Meier survival curves for each group. ITTACA has been developed to be a useful tool for comparing personal results to the existing results in the field of transcriptome studies with microarrays.

Proper citation: Integrated Tumor Transcriptome Array and Clinical data Analysis (RRID:SCR_008182) Copy   

•   Source: SciCrunch Registry

http://www.bh4.org/BH4DatabasesBiodef.asp

THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 26, 2016. The BIODEF database have tabulated the most common clinical and laboratory data related to hyperphenylalaninaemia and tetrahydrobiopterin deficiencies. Additionally, there are data regarding treatment, outcome, and DNA analysis. Approximately 2% of newborns with hyperphenylalaninaemia are deficient in tetrahydrobiopterin. Selective screening must be performed in all instances where hyperphenylalaninaemia is detected by neonatal screening. In the last 20 years, 308 patients with tetrahydrobiopterin deficiencies have been recognized as a result of screening carried out, worldwide, in Departments of Paediatrics. Of these 308 patients, 181 suffered from 6-pyruvoyltetrahydropterin synthase deficiency, 92 from dihydropteridine reductase deficiency, 13 from pterin-4a-carbinolamine dehydratase deficiency, 12 from GTP cyclohydrolase I deficiency, and 10 are still unclassified. The BIODEF database have tabulated the most common clinical and laboratory data related to hyperphenylalaninaemia and tetrahydrobiopterin deficiencies. Additionally, there are data regarding treatment, outcome, and DNA analysis. Preliminary evaluation reveals that the degree of hyperphenylalaninaemia can vary from normal to 2500 mumol/L. Analyses of pterins in urine and measurement of dihydropteridine reductase activity from Guthrie cards are absolutely essential tests for accurate diagnosis. There is a regional (demographic) variation in the frequency of tetrahydrobiopterin deficiencies indicating the highest incidence in Saudi Arabia, probably a consequence of the high consanguinity rate.

Proper citation: International Database of Tetrahydrobiopterin Deficiencies (RRID:SCR_008171) Copy   

•   Source: SciCrunch Registry

http://report.nih.gov/

A database of federally funded biomedical research projects conducted at universities, hospitals, and other research institutions that provides a central point of access to reports, data, and analyses of NIH research. The RePORTER has replaced the CRISP database. The database, maintained by the Office of Extramural Research at the National Institutes of Health, includes projects funded by the National Institutes of Health (NIH), Substance Abuse and Mental Health Services (SAMHSA), Health Resources and Services Administration (HRSA), Food and Drug Administration (FDA), Centers for Disease Control and Prevention (CDCP), Agency for Health Care Research and Quality (AHRQ), and Office of Assistant Secretary of Health (OASH).

Proper citation: National Institutes of Health Research Portfolio Online Reporting Tool (RRID:SCR_006874) Copy   

•   Source: SciCrunch Registry

http://www.nlm.nih.gov/pubs/factsheets/medline.html

MEDLINE (Medical Literature Analysis and Retrieval System Online) is the U.S. National Library of Medicine''s (NLM) premier bibliographic database that contains over 16 million references to journal articles in life sciences with a concentration on biomedicine. MEDLINE is the primary component of PubMed, part of the Entrez series of databases provided by NLM''s National Center for Biotechnology Information (NCBI). MEDLINE may also be searched via the NLM Gateway. Currently, citations from approximately 5,200 worldwide journals in 37 languages; 60 languages for older journals. Citations for MEDLINE are created by the NLM, international partners, and collaborating organizations. The subject scope of MEDLINE is biomedicine and health, broadly defined to encompass those areas of the life sciences, behavioral sciences, chemical sciences, and bioengineering needed by health professionals and others engaged in basic research and clinical care, public health, health policy development, or related educational activities. MEDLINE also covers life sciences vital to biomedical practitioners, researchers, and educators, including aspects of biology, environmental science, marine biology, plant and animal science as well as biophysics and chemistry. Sponsors: Services/products providing access to MEDLINE data are also developed and made available by organizations that lease the database from NLM.

Proper citation: National Library of Health: Medical Literature Analysis and Retrieval System Online Fact Sheet (RRID:SCR_006994) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/jhucis_pedatlas/

Anatomical atlases constructed by Computational Anatomy of Johns Hopkins University for analysis of shape vectors. The atlases were generated from segmented hippocampal and amygdala structures in acquired populations of children, adolescents and young adults in neuroimaging studies of major depression disorder (MDD) at Washington University at St Louis.

Proper citation: Atlases of amygdala and hippocampus for pediatric populations (RRID:SCR_014085) Copy   

•   Source: SciCrunch Registry

http://hb.flatironinstitute.org/

Formerly known as GIANT (Genome-scale Integrated Analysis of gene Networks in Tissues), HumanBase applies machine learning algorithms to learn biological associations from massive genomic data collections. These integrative analyses reach beyond existing "biological knowledge" represented in the literature to identify novel, data-driven associations.

Proper citation: HumanBase (RRID:SCR_016145) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/reliability/

Data collected from subjects scanned 3 times (V1, V2, V3), with V1 and V2 on a scanner, V3 on another scanner in another site. Resting state blood oxygenation level dependent functional MRI (BOLD fMRI), pseudo continuous arterial spin labeling (pCASL), and high resolution 3D T1 imaging were performed under eyes open (EO) and eyes closed (EC) conditions.

Proper citation: Intra- and inter-scanner reliability of RS-fMRI BOLD and ASL with eyes closed vs. eyes open (RRID:SCR_016935) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/pubs/MitoCarta/

Collection of genes encoding proteins with strong support of mitochondrial localization. Inventory of genes encoding mitochondrial-localized proteins and their expression across 14 mouse tissues. Database is based on human and mouse RefSeq proteins that are mapped to NCBI Gene loci. MitoCarta 2.0 inventory provides molecular framework for system-level analysis of mammalian mitochondria.

Proper citation: MitoCarta (RRID:SCR_018165) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.cgl.ucsf.edu/

Biomedical technology resource center that develops software and web-based resources for the visualization and analysis of molecular structure, and related data, at scales ranging from the atomic to the supramolecular. They create tools for handling and integrating diverse types of biomolecular data, including atomic-resolution coordinates, density maps, sequences, annotations, and networks. Their primary efforts are in the visualization and analysis of structures of molecules and molecular assemblies, enzyme sequence-structure-function relationships, and network representations of protein similarity, binding interactions, and biological pathways. They provide technologies to enable identifying the molecular bases of disease and phenotypic variation, annotating proteins of unknown function, identifying targets for drug development, designing drugs, and engineering proteins with new functions. RBVI distributes software tools, including the popular UCSF Chimera visualization and analysis package, develops and hosts the Structure-Function Linkage Database, and provides access to state-of-the-art computational resources in support of research projects in these areas.

Proper citation: Resource for Biocomputing Visualization and Informatics (RRID:SCR_001374) Copy   

•   Source: SciCrunch Registry

http://www.rstudio.com/shiny/

Open source R package that provides web framework for building web applications using R. Used to create interactive web apps in native R, without needing to use HTML, CSS, or JavaScript.

Proper citation: Shiny (RRID:SCR_001626) Copy   

•   Source: SciCrunch Registry

http://mzmatch.sourceforge.net/

A software to provide small tools for common processing tasks for LC/MS data. It is an extension to the metabolomics analysis pipeline mzMatch.R. The software is modular, open source, platform independent and written in Java.

Proper citation: mzMatch (RRID:SCR_000543) Copy   

•   Source: SciCrunch Registry

http://vortex.cs.wayne.edu/projects.htm#Onto-Design

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Many Laboratories chose to design and print their own microarrays. At present, the choice of the genes to include on a certain microarray is a very laborious process requiring a high level of expertise. Onto-Design database is able to assist the designers of custom microarrays by providing the means to select genes based on their experiment. Design custom microarrays based on GO terms of interest. User account required. Platform: Online tool

Proper citation: Onto-Design (RRID:SCR_000601) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/metagear/index.html

Software R package for research synthesis taxonomy from applying systematic review approach to assemble and screen literature, to extract data from studies, and to summarize and analyze these data with statistics of meta analysis.

Proper citation: metagear (RRID:SCR_017085) Copy   

•   Source: SciCrunch Registry

https://data.broadinstitute.org/alkesgroup/Eagle/

Software package for statistical estimation of haplotype phase either within a genotyped cohort or using a phased reference panel in large scale sequencing. The package includes Eagle1 (to harness identity-by-descent among distant relatives to rapidly call phase using a fast scoring approach) and Eagle2 (to analyze a full probabilistic model similar to the diploid Li-Stephens model used by previous HMM-based methods.

Proper citation: Eagle (RRID:SCR_015991) Copy   

•   Source: SciCrunch Registry