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

Software Python library that relies on the REST API provided by the XNAT platform since its 1.4 version. XNAT is an extensible database for neuroimaging data. The main objective is to ease communications with an XNAT server to plug-in external tools or python scripts to process the data.

Proper citation: pyxnat (RRID:SCR_002574) Copy   

•   Source: SciCrunch Registry

http://jaspar.genereg.net

Open source database of curated, non-redundant set of profiles derived from published collections of experimentally defined transcription factor binding sites for multicellular eukaryotes. Consists of open data access, non-redundancy and quality. JASPAR CORE is smaller set that is non-redundant and curated. Collection of transcription factor DNA-binding preferences, modeled as matrices. These can be converted into Position Weight Matrices (PWMs or PSSMs), used for scanning genomic sequences. Web interface for browsing, searching and subset selection, online sequence analysis utility and suite of programming tools for genome-wide and comparative genomic analysis of regulatory regions. New functions include clustering of matrix models by similarity, generation of random matrices by sampling from selected sets of existing models and a language-independent Web Service applications programming interface for matrix retrieval.

Proper citation: JASPAR (RRID:SCR_003030) Copy   

•   Source: SciCrunch Registry

http://www.brenda-enzymes.org/

Database for functional enzyme and ligand-related information maintained as part of the German ELIXIR Node. Provides advanced query systems, evaluation tools, and various visualization options for the detailed assessment of enzyme properties. Enzyme data in BRENDA are classified according to the Enzyme Commission (EC) nomenclature of IUBMB.

Proper citation: BRENDA (RRID:SCR_002997) Copy   

•   Source: SciCrunch Registry

http://prosite.expasy.org/

Database of protein families and domains that is based on the observation that, while there is a huge number of different proteins, most of them can be grouped, on the basis of similarities in their sequences, into a limited number of families. Proteins or protein domains belonging to a particular family generally share functional attributes and are derived from a common ancestor. It is complemented by ProRule, a collection of rules based on profiles and patterns, which increases the discriminatory power of profiles and patterns by providing additional information about functionally and/or structurally critical amino acids. ScanProsite finds matches of your protein sequences to PROSITE signatures. PROSITE currently contains patterns and profiles specific for more than a thousand protein families or domains. Each of these signatures comes with documentation providing background information on the structure and function of these proteins. The database is available via FTP.

Proper citation: PROSITE (RRID:SCR_003457) Copy   

•   Source: SciCrunch Registry

http://www.ensembl.org/

Collection of genome databases for vertebrates and other eukaryotic species with DNA and protein sequence search capabilities. Used to automatically annotate genome, integrate this annotation with other available biological data and make data publicly available via web. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species.

Proper citation: Ensembl (RRID:SCR_002344) Copy   

•   Source: SciCrunch Registry

http://www.controlled-trials.com

Free-to-view clinical trials register of clinical trials worldwide, it allows users to search, register and share information about randomized controlled trials. Publication services are also available via the range of open access peer-reviewed journals published by BioMed Central. Current Controlled Trials is run by an editorial and technical in-house team. It receives advice from an international Advisory Group, including academics, doctors and health care specialists of international renown. The Advisory Group provides valuable guidance on the current activities and possible new directions of Current Controlled Trials' two databases, the metaRegister of Controlled Trials (mRCT) and the International Standard Randomised Controlled Trial Number (ISRCTN) scheme.

Proper citation: Current Controlled Trials (RRID:SCR_002325) Copy   

•   Source: SciCrunch Registry

http://www.bork.embl.de/j/

The main focus of this Computational Biology group is to predict function and to gain insights into evolution by comparative analysis of complex molecular data. The group currently works on three different scales: * genes and proteins, * protein networks and cellular processes, and * phenotypes and environments. They require both tool development and applications. Some selected projects include comparative gene, genome and metagenome analysis, mapping interactions to proteins and pathways as well as the study of temporal and spatial protein network aspects. All are geared towards the bridging of genotype and phenotype through a better understanding of molecular and cellular processes. The services - resources & tools, developed by Bork Group, are mainly designed and maintained for research & academic purposes. Most of services are published and documented in one or more papers. All our tools can be completely customized and integrated into your existing framework. This service is provided by the company biobyte solutions GmbH. Please visit their tools and services pages for full details and more information. Standard commercial licenses for our tools are also available through biobyte solutions GmbH. The group is partially associated with Max Delbr��ck Center for Molecular Medicine (MDC), Berlin.

Proper citation: EMBL - Bork Group (RRID:SCR_000810) Copy   

•   Source: SciCrunch Registry

http://www.geuvadis.org/web/geuvadis/home

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 6,2023. A European Medical Sequencing Consortium committed to gaining insights into the human genome and its role in health and medicine by sharing data, experience and expertise in high-throughput sequencing., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GEUVADIS (RRID:SCR_000684) Copy   

•   Source: SciCrunch Registry

http://www.knockoutmouse.org/about/eucommtools

Functional Annotation of the Mouse Genome, it will complete the International Knockout Mouse Consortium (IKMC) resource of mutations for all protein coding genes. Furthermore, it will maximize the utility of the conditional IKMC resource by generating up to 250 different, mostly inducible Cre driver mouse lines. In addition, EUCOMMTOOLS will develop novel tools to enhance the versatility of the IKMC resource. EUCOMMTOOLS vectors, mutant ES cells and mutant mice are distributed worldwide: EUCOMMTOOLS mutant ES cells and vectors can be obtained from the European Mouse Mutant Cell Repository (EuMMCR). EUCOMMTOOLS mutant mice are archived and distributed by the European Mouse Mutant Archive (EMMA). Knockout-first Mutant Alleles: EUCOMMTOOLS will create 3500 C57Bl/6 conditional mutant alleles for single-exon (or otherwise previously conditionally untargeted) protein-coding mouse genes. These alleles will be made predominantly by introducing an "artificial intron", containing a standard EUCOMM promoter-driven targeting cassette, into the coding sequence of the single-exon gene. Cre Resources: EUCOMMTOOLS will engineer 500 new Cre C57Bl/6 ES cell lines by Cre knock-ins into genes with useful expression patterns. The resource will be made with inducible forms of Cre recombinase such as CreERT2. Up to 250 lines of Cre driver mice on a pure C57Bl/6N background will be generated and the Cre expression patterns documented and annotated in day P14 and P56. These mice will form a matched Cre driver resource for C57Bl/6N mice produced from conditional IKMC resources. Research, Technology and Complementary Reagents: EUCOMMTOOLS will develop novel technologies to add value, depth and flexibility to existing IKMC ES cell and mouse resources. Key areas include: * Development of novel recombinase based regulatory switches * Exploration of zinc-finger nuclease stimulated homologous recombination strategies in fertilized oocytes * Development and validation of complementary modular vector reagents which enable the construction of new useful knock-in alleles such as fluorescent and other reporters, site specific recombinases, and mutant cDNAs. These novel alleles can be constructed either by re-utilizing existing IKMC modular vector resources or directly modifying existing targeted IKMC ES cell lines by RMCE.

Proper citation: EUCOMMTOOLS (RRID:SCR_000676) Copy   

•   Source: SciCrunch Registry

http://zebrafishucl.org/zebrafishbrain#about-1

Collates and curates neuroanatomical data and information generated both in-house and by community to communicate current state of knowledge about neuroanatomical structures in developing zebrafish. Most of data come from high resolution confocal imaging of intact brains in which neuroanatomical structures are labelled by combinations of transgenes and antibodies. Community repository for image based data related to neuroanatomy of zebrafish.

Proper citation: Zebrafish Brain Atlas (RRID:SCR_000606) Copy   

•   Source: SciCrunch Registry

http://search.driver.research-infrastructures.eu/

Data infrastructure project that merged with OpenAIRE. Cohesive, robust and flexible, pan-European infrastructure for digital repositories, offering sophisticated services and functionalities for researchers, administrators and the general public. Access the network of freely accessible digital repositories with content across academic disciplines with over 3,500,000 scientific publications, found in journal articles, dissertations, books, lectures, reports, etc., harvested regularly from more than 295 repositories, from 38 countries. DRIVER has established a network of relevant experts and Open Access repositories. DRIVER-II will consolidate these efforts and transform the initial testbed into a fully functional, state-of-the art service, extending the network to a larger confederation of repositories. It aims to optimize the way the e-Infrastructure is used to store knowledge, add value to primary research data and information making secondary research more effective, provide a valuable asset for industry, and help bridging research and education. The objectives of DRIVER-II, the second phase of the project, include efforts to expand, enrich, and strengthen the results of DRIVER, in the following areas: * strategic geographic and community expansion by means of the DRIVER confederation * establish a robust, scalable repository infrastructure accompanied by an open source software package D-Net * broader coverage of content through the use of enhanced publications * advanced end-user functionality to support scientific exploration of complex digital objects * larger outreach and advocacy programs * continued repository support * guidelines for interoperability in the larger European digital library community

Proper citation: Digital Repository Infrastructure Vision for European Research (RRID:SCR_002752) Copy   

•   Source: SciCrunch Registry

http://degradome.uniovi.es

A database of human, chimpanzee, mouse, and rat proteases and protease inhibitors, as well as as the growing number of hereditary diseases caused by mutations in protease genes. Analysis of the human and mouse genomes has allowed us to annotate 581 human, 580 chimpanzee, 667 mouse, and 655 rat protease genes. Proteases are classified in five different classes according to their mechanism of catalysis. Proteases are a diverse and important group of enzymes representing >2% of the human, chimpanzee, mouse and rat genomes. This group of enzymes is implicated in numerous physiological processes. The importance of proteases is illustrated by the existence of 99 different hereditary diseases due to mutations in protease genes. Furthermore, proteases have been implicated in multiple human pathologies, including vascular diseases, rheumatoid arthritis, neurodegenerative processes, and cancer. During the last ten years, our laboratory has identified and characterized more than 60 human protease genes. Due to the importance of proteolytic enzymes in human physiology and pathology, we have recently introduced the concept of Degradome, as the complete repertoire of proteases expressed by a tissue or organism. Thanks to the recent completion of the human, chimpanzee, mouse, and rat genome sequencing projects, we were able to analyze and compare for the first time the complete protease repertoire in those mammalian organisms, as well as the complement of protease inhibitor genes. This webpage also contains the Supplementary Material of Human and mouse proteases: a comparative genomic approach Nat Rev Genet (2003) 4: 544-558, Genome sequence of the brown Norway rat yields insights into mammalian evolution Nature (2004) 428: 493-521, A genomic analysis of rat proteases and protease inhibitors Genome Res. (2004) 14: 609-622, and Comparative genomic analysis of human and chimpanzee proteases Genomics (2005) 86: 638-647.

Proper citation: Mammalian Degradome Database (RRID:SCR_007624) 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

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

http://www.ihop-net.org/UniPub/iHOP/

Information system that provides a network of concurring genes and proteins extends through the scientific literature touching on phenotypes, pathologies and gene function. It provides this network as a natural way of accessing millions of PubMed abstracts. By using genes and proteins as hyperlinks between sentences and abstracts, the information in PubMed can be converted into one navigable resource, bringing all advantages of the internet to scientific literature research. Moreover, this literature network can be superimposed on experimental interaction data (e.g., yeast-two hybrid data from Drosophila melanogaster and Caenorhabditis elegans) to make possible a simultaneous analysis of new and existing knowledge. The network contains half a million sentences and 30,000 different genes from humans, mice, D. melanogaster, C. elegans, zebrafish, Arabidopsis thaliana, yeast and Escherichia coli.

Proper citation: Information Hyperlinked Over Proteins (RRID:SCR_004829) Copy   

•   Source: SciCrunch Registry

http://www.erasmusmc.nl/pathologie/clinicalpathology/tissuebank/161255/?lang=en

The Erasmus MC Virtual Tissue Bank is embedded in the department of Pathology. The collection is meant for medical research purposes only. This concerns a typical clinical based pathology biobank. Tissue samples left over from surgical resection specimen are stored under liquid nitrogen and can be requested by Erasmus MC scientists for medical scientific experiments. An application has been developed to enable scientists to search the collection on-line and request tissue samples over the Erasmus MC Intranet. Every request shall be judged according to procedures determined by the Erasmus MC Tissue Bank. A growing need is anticipated for large collections of well-diagnosed fresh frozen tumor tissue and, if available, corresponding pre-malignant and normal tissue samples. Scientific research on patient residual material has to comply with strict rules and regulations. Equipment The Erasmus MC Tissue bank manages the PALM microdissection laser for the center for Biomics, which is available through the center for Biomics ONLY after having followed an introduction course. Additionally, a complete TMA (Tissue Micro Array) platform, fully funded by the Josephine Nefkens Stichting, consisting of a Beecher Automated Tissue Arrayer ATA 27 and a Virtual Microscope or Nanozoomer from Hamamatsu and Medical Solutions with TMA analyses software strongly supports translational research on tissue samples. Complete histologic Images from the Virtual Microscope are available within the Erasmus MC Intranet or available on the Internet either by overview or a direct example.

Proper citation: Erasmus MC Tissue Bank (RRID:SCR_004945) 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

http://www.informatics.jax.org/home/recombinase

Curated data about all recombinase-containing transgenes and knock-ins developed in mice providing a comprehensive resource delineating known activity patterns and allows users to find relevant mouse resources for their studies.

Proper citation: Recombinase (cre) Activity (RRID:SCR_006585) 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://www.glycosciences.de/glycocd/

Manually curated, comprehensive repository of clusters of differentiation (CDs) which are a) defined as distinct oligosaccharide sequences as part of either glycoproteins and/or glycosphingolipids and b) defined as proteins which have carbohydrate recognition sites (CRDs) or as carbohydrate binding lectins. The data base is generated by exhaustive search of literature and other online data banks related to carbohydrates and proteins. This data bank is the beginning of an effort to provide concise, relevant information of carbohydrate-related CDs in a user- friendly manner. For users convenience the data bank under menu browse of GlycoCD is arranged in two section namely carbohydrate recognition CDs (CRD CD) and glycan CD. The carbohydrate recognition CD part is the collection of proteins which recognize glycan structures by means of the CRDs. Glycan CD is the part in which CDs are summarized which characterize specific oligosaccharide structures. The GlycoCD databank has been developed with the aim to assist the immunologist, cell biologist as well as the clinician who wants to keep up with the present knowledge in this field of glycobiology.

Proper citation: Glyco-CD (RRID:SCR_001574) Copy   

•   Source: SciCrunch Registry