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Portuguese distributed infrastructure for biological data and Portuguese node of ELIXIR.
Proper citation: BioData Management Portal (RRID:SCR_023138) Copy
Astronomical data archive focused on optical, ultraviolet, and near infrared. Used for maximizing scientific accessibility and productivity of astronomical data. MAST hosts data from over dozen missions like Webb, Hubble, TESS, Kepler, and in the future Roman.
Proper citation: Barbara A. Mikulski Archive for Space Telescopes (RRID:SCR_023137) Copy
http://purl.bioontology.org/ontology/ACGT-MO
Ontology to represent the domain of cancer research and management in a computationally tractable manner.
Proper citation: Cancer Research and Management ACGT Master Ontology (RRID:SCR_006953) Copy
http://www.evidenceontology.org
A controlled vocabulary that describes types of scientific evidence within the realm of biological research that can arise from laboratory experiments, computational methods, manual literature curation, and other means. Researchers can use these types of evidence to support assertions about research subjects that result from scientific research, such as scientific conclusions, gene annotations, or other statements of fact. ECO comprises two high-level classes, evidence and assertion method, where evidence is defined as a type of information that is used to support an assertion, and assertion method is defined as a means by which a statement is made about an entity. Together evidence and assertion method can be combined to describe both the support for an assertion and whether that assertion was made by a human being or a computer. However, ECO can not be used to make the assertion itself; for that, one would use another ontology, free text description, or other means. ECO was originally created around the year 2000 to support gene product annotation by the Gene Ontology. Today ECO is used by many groups concerned with provenance in scientific research. ECO is used in AmiGO 2
Proper citation: ECO (RRID:SCR_002477) Copy
http://dynamine.ibsquare.be/submission/
An NMR based method for protein folding prediction. Users can enter a UniProt identifier, FASTA sequences, or upload a file containing FASTA sequences and results are returned., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: DynaMine (RRID:SCR_014559) Copy
https://www.iveindhoven.com/en/article/reichert-jung-ultracut-e-ultramicrotome/
Reichert Jung Ultracut E, article number 131-960, is used to cut ultrathin and semithin sections of resin embedded samples for electron microscopy.
Proper citation: Ultracut: E ultramicrotome (RRID:SCR_022980) Copy
https://omictools.com/3omics-tool
THIS RESOURCE IS NO LONGER IN SERVICE, documented October 19, 2016. A web tool for visualizing and integrating multiple inter- or intra-transcriptomic, proteomic, and metabolomic human data. 3Omics generates inter-omic correlation networks to visualize relationships in data with respect to time or experimental conditions for transcripts, proteins and metabolites.
Proper citation: 3Omics (RRID:SCR_014678) Copy
Software suite to analyse gait trials collected with Experimental Dynamic Gait Arena for Rodents. Used for rodent gait analysis.
Proper citation: GAITOR Suite (RRID:SCR_023031) Copy
The Precellys 24 homogenizer with automatic tube locking system with the ability to process up to 24 tubes simultaneously., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Bertin Technologies: Precellys 24 tissue homogenizer (RRID:SCR_022979) Copy
https://www.emkatech.com/product/iox2-software/
Software tool to acquire, analyze, view, and store physiological data generated during preclinical experiment. Has library of application specific analysis modules for real time signal processing.
Proper citation: IOX2 (RRID:SCR_022973) Copy
https://www.inscopix.com/nvoke
Miniature microscope system that integrates in vivo cellular resolution calcium imaging with simultaneous or sequential optogenetic manipulation to causally link neural circuit activity with behavior.
Proper citation: iNSCOPIX: nVoke System (RRID:SCR_023028) Copy
https://open-brain-consent.readthedocs.io/en/stable/
Platform for informing research participants and obtaining consent to share brain imaging data. Provides suggested wording/templates for MRI studies human participant consent forms (including GDPR version), reference of tools for data anonymization, etc to make prospective data sharing possible.
Proper citation: Open Brain Consent (RRID:SCR_022972) Copy
http://purl.bioontology.org/ontology/CPTAC
A basic ontology which describes the proteomics pipeline infrastructure for CPTAC project
Proper citation: CPTAC Proteomics Pipeline Infrastructure Ontology (RRID:SCR_006945) Copy
https://labsyspharm.github.io/jekyll-tutorial/
Website tutorial for creating Jekyll-based scientific website, including editing in GitHub, working locally with Jekyll and applying Jekyll and Markdown formatting basics, and using custom themes.
Proper citation: Jekyll Tutorial (RRID:SCR_022859) Copy
https://www.pacemweb.nl/simulation/assessment-settings
Web tool for aggregate consumer exposure assessment. Model is based on realistic product usage information obtained from surveys. Information on usage, frequency and amount of personal care products and household cleaning products in various European countries is included.
Proper citation: PACEMweb (RRID:SCR_023083) Copy
http://ml-neuronbrowser.janelia.org/
Interactive web platform for anyone to explore, search, filter and visualize the single neuron reconstructions.
Proper citation: MouseLight Neuron Browser (RRID:SCR_016669) Copy
A database and collaboration tool which allows researchers to make contacts or find collaborators within their field or from a different discipline. Users can create a profile detailing their collaboration interests, research areas, and methodologies as well as add links to external sites such as LinkedIn and Academia.edu. Piirus takes the information from users' profiles to suggest researchers with whom they may be interested in collaborating with. Users can also search for users with particular interests, expertise, or techniques.
Proper citation: Piirus (RRID:SCR_013964) Copy
https://github.com/linnarsson-lab/loom-viewer
Software tool for sharing, browsing and visualizing single-cell data stored in the Loom file format.
Proper citation: loom-viewer (RRID:SCR_016683) Copy
https://bdcw.org/MetGENE/index.php
Web tool identifies associations between genes and metabolites that are biosynthesized, metabolized, or transported by proteins coded by genes. Gene centric metabolomics information retrieval tool. Knowledge based, gene centric data aggregator that hierarchically retrieves information about genes, their related pathways, reactions,metabolites, and metabolomic studies from standard data repositories under one dashboard to enable ease of access through centralization of relevant information. Information can be contextualized by filtering along species, anatomy tissue and disease or phenotype.
Proper citation: MetGENE (RRID:SCR_023402) Copy
https://github.com/hetio/hetmatpy
Software Python package for matrix storage and operations on hetnets. Enables identifying relevant network connections between set of query nodes.
Proper citation: HetMatPy (RRID:SCR_023409) Copy
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