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http://www.softberry.com/

Developer of software tools for genomic research focused on computational methods of high throughput biomedical data analysis, including software to support next generation sequencing technologies, transcriptome analysis with RNASeq data, SNP detection and selection of disease specific SNP subsets. Provides custom genome annotation services.

Proper citation: SoftBerry (RRID:SCR_000902) Copy   

•   Source: SciCrunch Registry

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://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

https://www.bioinfor.com/peaks-studio/

Software platform with complete solutions for discovery proteomics, including protein identification and quantification, analysis of post translational modifications and sequence variants (mutations), and peptide/protein de novo sequencing.

Proper citation: PEAKS Studio (RRID:SCR_022841) Copy   

•   Source: SciCrunch Registry

http://www.bioquest.org/esteem/esteem_details.php?product_id=248

Software to allow construction, analysis, and simulation of complex models in spreadsheet format.

Proper citation: PopTools (RRID:SCR_022840) Copy   

•   Source: SciCrunch Registry

http://www.rad.upenn.edu/sbia/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 2, 2023. A section of the Penn department of radiology, it is devoted to the development of computer-based image analysis methods and their application to clinical research studies. Image analysis methodologies include image registration, segmentation, population-based statistical analysis, biophysical modeling of anatomical deformations, and high-dimensional pattern classification. Clinical research studies spans a variety of clinical areas and organs, and they include brain diseases such as Alzheimer's disease and schizophrenia, evaluation of treatment effects in large clinical trials, diagnosis of cardiac diseases, and diagnosis prostate, breast and brain cancer. SBIA also performs small animal imaging research aiming to understand brain development in mouse models. It has multiple resources which can be accessed by researcher.

Proper citation: SBIA (RRID:SCR_013628) 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.vanderbilt.edu/vinse/facilities/instruments/xps+phi+5000-versaprobe

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 13,2025.Lab with access to the PHI Versaprobe, a surface-sensitive analytical tool for identifying elemental composition and local bonding environment.

Proper citation: Vanderbilt X-Ray Photoelectron Spectroscopy Lab (RRID:SCR_000897) Copy   

•   Source: SciCrunch Registry

http://panomics.pnnl.gov/

Biomedical technology research center that develops and integrates new proteomic technologies for collaborative and service studies, disseminating the new technologies and training scientists in their use.

Proper citation: Proteomics Research Center for Integrative Biology (RRID:SCR_001098) Copy   

•   Source: SciCrunch Registry

http://www.eecs.qmul.ac.uk/mmv/datasets/deap/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 12,2025. Multimodal dataset for emotion analysis using EEG, Physiological and Video Signals of human affective states. The electroencephalogram (EEG) and peripheral physiological signals of 32 participants were recorded as each watched 40 one-minute long excerpts of music videos. Participants rated each video in terms of the levels of arousal, valence, like/dislike, dominance and familiarity. For 22 of the 32 participants, frontal face video was also recorded. A novel method for stimuli selection was used, utilizing retrieval by affective tags from the last.fm website, video highlight detection and an online assessment tool. The dataset is made publicly available and other researchers are encouraged to use it for testing their own affective state estimation methods.

Proper citation: DEAPdataset (RRID:SCR_001586) Copy   

•   Source: SciCrunch Registry

http://www.broad.mit.edu/mpr/lung

Data set of a molecular taxonomy of lung carcinoma, the leading cause of cancer death in the United States and worldwide. Using oligonucleotide microarrays, researchers analyzed mRNA expression levels corresponding to 12,600 transcript sequences in 186 lung tumor samples, including 139 adenocarcinomas resected from the lung. Hierarchical and probabilistic clustering of expression data defined distinct sub-classes of lung adenocarcinoma. Among these were tumors with high relative expression of neuroendocrine genes and of type II pneumocyte genes, respectively. Retrospective analysis revealed a less favorable outcome for the adenocarcinomas with neuroendocrine gene expression. The diagnostic potential of expression profiling is emphasized by its ability to discriminate primary lung adenocarcinomas from metastases of extra-pulmonary origin. These results suggest that integration of expression profile data with clinical parameters could aid in diagnosis of lung cancer patients.

Proper citation: Classification of Human Lung Carcinomas by mRNA Expression Profiling Reveals Distinct Adenocarcinoma Sub-classes (RRID:SCR_003010) Copy   

•   Source: SciCrunch Registry

http://lab.rockefeller.edu/chait/

Biomedical technology research center that develops cutting-edge mass spectrometric tools for analyzing peptides and proteins. It makes its software tools developed for data analysis freely available.

Proper citation: National Resource for the Mass Spectrometric Analysis of Biological Macromolecules (RRID:SCR_009007) 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://platform.cerebellum.neuroinf.jp/

THIS RESOURCE IS NO LONGER IN SERVICE, documented January 13, 2022. Digital research archive for cerebellar research including mini-reviews of contemporary cerebellar research, list of papers and mathematical models for cerebellar operation.

Proper citation: Cerebellar Platform (RRID:SCR_001700) 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