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http://www.innomed-addneuromed.com/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9,2023. Project portal for a cross European study designed to find biomarkers, or tests, for Alzheimer's disease. Its objectives are to produce and improve experimental models of Alzheimer's for biomarker discovery and to identify a biomarker for Alzheimer's disease suitable for diagnosis, prediction, and monitoring disease progression for use in clinical trials and in clinical practice. The baseline dataset database was scheduled to be completed and locked in 2008 and become available to researchers by 2009. Requests to access the data will be reviewed by the scientific projects committee.

Proper citation: AddNeuroMed (RRID:SCR_003819) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/pdbe/

The European resource for the collection, organization and dissemination of data on biological macromolecular structures. In collaboration with the other worldwide Protein Data Bank (wwPDB) partners - the Research Collaboratory for Structural Bioinformatics (RCSB) and BioMagResBank (BMRB) in the USA and the Protein Data Bank of Japan (PDBj) - they work to collate, maintain and provide access to the global repository of macromolecular structure data. The main objectives of the work at PDBe are: * to provide an integrated resource of high-quality macromolecular structures and related data and make it available to the biomedical community via intuitive user interfaces. * to maintain in-house expertise in all the major structure-determination techniques (X-ray, NMR and EM) in order to stay abreast of technical and methodological developments in these fields, and to work with the community on issues of mutual interest (such as data representation, harvesting, formats and standards, or validation of structural data). * to provide high-quality deposition and annotation facilities for structural data as one of the wwPDB deposition sites. Several sophisticated tools are also available for the structural analysis of macromolecules.

Proper citation: PDBe - Protein Data Bank in Europe (RRID:SCR_004312) Copy   

•   Source: SciCrunch Registry

http://www.rhea-db.org/

Manually annotated reaction database where all reaction participants (reactants and products) are linked to the ChEBI database (Chemical Entities of Biological Interest) which provides detailed information about structure, formula and charge. Rhea provides built-in validations that ensure both elemental and charge balance of the reactions. The database has been populated with the reactions found in the Enzyme Commission (EC) list (and in the IntEnz and ENZYME databases), extending it with additional known reactions of biological interest. While the main focus of Rhea is enzyme-catalyzed reactions, other biochemical reactions are also included. Rhea is a manually annotated resource and it provides: stable reaction identifiers for each of its reactions; directionality information if the physiological direction of the reaction is known; the possibility to link several reactions together to form overall reactions; extensive cross-references to other resources including enzyme-catalyzed and other metabolic reactions, such as the EC list (in IntEnz), KEGG, MetaCyc and UniPathway; and chemical substructure and similarity searches on compounds in Rhea.

Proper citation: RHEA (RRID:SCR_004713) Copy   

•   Source: SciCrunch Registry

http://athina.biol.uoa.gr/PRED-CLASS/

A system of cascading neural networks that classifies any protein, given its amino acid sequence alone, into one of four possible classes: membrane, globular, fibrous, mixed.

Proper citation: PRED-CLASS (RRID:SCR_006216) Copy   

•   Source: SciCrunch Registry

http://tomcat.esat.kuleuven.be/txtgate/

TXTGate is a literature index database and is part of an experimental platform to evaluate (combinations of) information extraction and indexing from a variety of biological annotation databases. It is designed towards the summarization and analysis of groups of genes based on text. By means of tailored vocabularies, selected textual fields and MedLine abstracts of LocusLink and SGD are indexed. Subclustering and links to external resources allow for an in-depth analysis of the resulting term profiles. You need to be registered in order to use the TXTGate application. Platform: Online tool

Proper citation: TXTGate (RRID:SCR_005812) Copy   

•   Source: SciCrunch Registry

https://github.com/DiltheyLab/HLA-LA

Software implements new graph alignment model for human leukocyte antigen, based on projection of linear alignments onto variation graph. Enables accurate HLA type inference from whole genome and whole exome Illumina data; from long-read Oxford Nanopore and Pacific Biosciences data and from genome assemblies.

Proper citation: HLA-LA (RRID:SCR_022283) Copy   

•   Source: SciCrunch Registry

https://biofam.github.io/MOFA2/

Software framework for unsupervised integration of multi-omics data sets. Used for discovering principal sources of variation in multi omics data sets.

Proper citation: MOFA (RRID:SCR_022992) Copy   

•   Source: SciCrunch Registry

http://simbioms.org/

SIMBioMS (System for Information Management in BioMedical Studies) is a multi-module solution for data management in biomedical studies. Any research concerning human samples and/or utilizing high-throughput technologies yields such amount of information that conventional data storage solution might not be sufficient. We offer here three software modules: * Sample Information Management System (SIMS), * Assay Information Management System (AIMS) * Sample avAILability system (SAIL) * Emanta Administration tool (Emanta) All three software modules were developed as a part of the integrated EU project MolPAGE (Molecular Phenotyping to Accelerate Genomic Epidemiology) and the collaborative research project ENGAGE (European Network of Genomic and Genetic Epidemiology). SIMS and AIMS can work either as united system or as two completely independent components. In turn, SAIL is an independent web-based system for indexing of phenotypes availability in different cohorts and collections. All systems are packaged in such a way that they can easily be installed either as local (e.g. on a laptop) or as centralized databases (to be used by a group of people). SIMS and AIMS benefit from customizable interface, editable vocabularies and a choice of options for tackling data confidentiality issues. The systems provides a user with efficient means of control over data exchange process and at the same time helps to format the metadata in compliance with the standards accepted in functional genomics. Since SIMBioMS is an open source project, source files can be downloaded and changed by the user if needed.

Proper citation: SIMBioMS (RRID:SCR_005745) Copy   

•   Source: SciCrunch Registry

http://cordis.europa.eu/project/rcn/98370_en.html

The Colon Therapy Research (COLTHERES) consortium brings together clinical centers and translational researchers funded in the European Union to define and perform biomarker driven clinical trials to improve cancer therapy outcomes. This 4-year consortium will use comprehensively molecularly-annotated colon cancers as a "test-bed" to define specific biomarkers of response or resistance to signaling pathway agents.

Proper citation: Colon Therapy Research Consortium (COLTHERES) (RRID:SCR_013690) Copy   

•   Source: SciCrunch Registry

http://www.bibsonomy.org

A software application which assists in managing and sharing scientific literature. Users can collect and share publications, collaborate with other researchers, and find new resources and publications for research.

Proper citation: BibSonomy (RRID:SCR_013756) Copy   

•   Source: SciCrunch Registry

https://github.com/ledancs/hFigures

A Javascript library that aims to deliver a starting point for interactive health data visualization. Examples and demos are available on the site. hFigures was built with d3.js and a copy of the library is included in this repository. All rights and license terms apply to the d3.js library accordingly.

Proper citation: hFigures (RRID:SCR_014201) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=APIS

Software R package to assign offspring to their parents without any prior information other than offspring and parental genotypes, and user-defined, acceptable error rate among assigned offspring. Auto-adaptive parentage inference software that tolerates missing parents.

Proper citation: APIS (RRID:SCR_025445) Copy   

•   Source: SciCrunch Registry

https://lsbr.niams.nih.gov/bsoft/

Software package and a platform for the processing of electron micrographs in structural biology. Supports different image file formats used in electron microscopy (including MRC, SPIDER, IMAGIC, SUPRIM, and PIF)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Bsoft (RRID:SCR_016503) Copy   

•   Source: SciCrunch Registry

http://scipion.i2pc.es/

Software framework for image processing to obtain 3D models of macromolecular complexes using Electron Microscopy. Open-source project for integration, reproducibility and validation in 3D electron microscopy. It integrates several software packages to execute workflows combining different software tools, while taking care of formats and conversions. Electron Microscopy (3DEM). waiting for pdf from Joe

Proper citation: SCIPION (RRID:SCR_016738) Copy   

•   Source: SciCrunch Registry