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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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cafe variome Resource Report Resource Website 10+ mentions |
cafe variome (RRID:SCR_006162) | Cafe Variome | service resource, data or information resource, data set, data repository, storage service resource | Clearinghouse and exchange portal for gene variant (mutation) data produced by diagnostics laboratories, offering users a portal through which to announce, discover and acquire a comprehensive listing of observed neutral and disease-causing gene variants in patients and unaffected individuals. Cafe Variome is not a ''''database'''' for the hosting/display/release of data, but a shop window for finding data. As such, it holds only core info for each record, and uses this merely to enable holistic searching across resources. Diagnostics laboratories routinely assess DNA samples from patients with various inherited disorders, and so produce a great wealth of data on the genetic basis of disease. Unfortunately, those data are not usually shared with others. To address this gross deficiency, a novel system has been developed that aims to facilitate the automated transfer of diagnostic laboratory data to the wider community, via an internet based Cafe for routinely exchanging genetic variation data. The flow of research data concerning the genetic basis of health and disease is critical to understanding and developing treatments for a range of genetic diseases. Overall, the project aims to lower the barriers and provide incentives for a willing community to share data, and thereby facilitate the broader exploitation of diagnostic laboratory data. Cafe Variome aims to address the above data flow problems by: # Minimizing the effort required to publish variant data # Ensuring attribution for data creators working in diagnostic laboratories Key elements of the project strategy are: * Data publication will be automated by endowing standard analysis tools used by laboratories with an online data submission function. Submissions will be received by a central Internet depot, which will serve as a place where published datasets are advertised, and subsequently discovered by diverse 3rd parties. * Each dataset will be unambiguously linked with the data submitter''''s identity, and systems devised to facilitate citation of published variant datasets so they can be cited in the literature. Data creators will thus be credited for their contributions. Data submitters can use Cafe Variome to simply announce or publicize their data to the world. To enable this, only core, non-identifiable data is submitted to the central repository, enabling users to search and discover records of interest in the source repository. The data are not automatically handed on to the user (unless intended by the submitters). Hence, the concept is used to deal with the challenge of maximally sharing data whilst fully respecting ethico-legal considerations. | phenotype, gene variant, mutation, gene, normal, disease | has parent organization: University of Leicester; Leicester; United Kingdom | Diseased, Healthy | European Union FP7/2007-2013- the GEN2PHEN project | Open access, Restricted access and Linked access | nlx_151664 | SCR_006162 | 2026-08-12 10:49:22 | 11 | ||||||
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Amazon Web Services Public Data Sets Resource Report Resource Website 1+ mentions |
Amazon Web Services Public Data Sets (RRID:SCR_006318) | AWS Public Data Sets | service resource, data or information resource, data set, data repository, storage service resource | A multidisciplinary repository of public data sets such as the Human Genome and US Census data that can be seamlessly integrated into AWS cloud-based applications. AWS is hosting the public data sets at no charge for the community. Anyone can access these data sets from their Amazon Elastic Compute Cloud (Amazon EC2) instances and start computing on the data within minutes. Users can also leverage the entire AWS ecosystem and easily collaborate with other AWS users. If you have a public domain or non-proprietary data set that you think is useful and interesting to the AWS community, please submit a request and the AWS team will review your submission and get back to you. Typically the data sets in the repository are between 1 GB to 1 TB in size (based on the Amazon EBS volume limit), but they can work with you to host larger data sets as well. You must have the right to make the data freely available. | astronomy, biology, chemistry, climatology, economics, encyclopedia, dictionary, mathematics, data collection platform, data sharing, geography, data archive |
is listed by: re3data.org is listed by: DataCite has parent organization: Amazon Web Services |
Public, The community can contribute to this resource | nlx_152013, r3d100010855 | https://doi.org/10.17616/R3M91V | SCR_006318 | Public Data Sets on AWS | 2026-08-12 10:49:24 | 1 | ||||||
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Johns Hopkins Point of Care Guides Resource Report Resource Website 1+ mentions |
Johns Hopkins Point of Care Guides (RRID:SCR_006314) | Johns Hopkins POC-IT Guides | data or information resource, database, software application, software resource, mobile app | Authoritative, need-to-know information from Johns Hopkins available for mobile devices and the web. Guides provide up to date information and break down details of diagnosis, drug indications, dosing, pharmacokinetics, side effects and interactions, pathogens, management, and vaccines into frequently-updated, quick-read entries. Available for infectious disease (ABX), diabetes, and HIV. | point of care, antibiotic, pathogen, infectious disease, drug, clinical test, management, complication, medication, clinical, infection, resistance | is related to: ABX Guide | Diabetes, Infectious disease, HIV | Available for purchase | nlx_151999 | SCR_006314 | Johns Hopkins Medicine POC-IT Guides, Johns Hopkins Guides: Antibiotic HIV and Diabetes Guides, POC-IT Guides | 2026-08-12 10:49:24 | 2 | ||||||
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General Neural Simulation System Resource Report Resource Website 100+ mentions |
General Neural Simulation System (RRID:SCR_006316) | GENESIS | software library, data or information resource, simulation software, narrative resource, software toolkit, source code, training material, software application, data set, software resource | General purpose simulation platform developed to support the simulation of neural systems ranging from subcellular components and biochemical reactions to complex models of single neurons, simulations of large networks, and systems-level models. As such, GENESIS, and its version for parallel and networked computers (PGENESIS) was the first broad scale modeling system in computational biology to encourage modelers to develop and share model features and components. User contributed GENESIS models and simulations are available. You may to contribute a model or simulation. Educational tutorials for instruction in both neurobiology and computational methods have been developed. These tutorials and GENESIS are now being widely used in graduate and undergraduate instruction. These uses include full semester courses in computational neuroscience or neural modeling, short intensive courses or workshops, an option for a course project, and short units on computational neuroscience within courses on artificial neural nets. They also have a repository of user-contributed tutorials and materials for use in neuroscience education. If you have course descriptions, syllabi, exercises, tutorials, or short HOWTO documents, please upload them to Education. | electrophysiology, computer, in silico, model, modeling, simulation, neural system, network, neurobiology, computational neuroscience, neural modeling, subcellular, biochemical reaction, neuron, channel, cell, FASEB list |
is related to: GENESIS Neural Database and Modelers Workspace is related to: ChannelDB is related to: Topographica has parent organization: University of Texas at San Antonio; Texas; USA is parent organization of: The Book of GENESIS |
The community can contribute to this resource | nif-0000-00091 | http://www.nitrc.org/projects/genesis http://genesis-sim.org/GENESIS/ | SCR_006316 | GENESIS, GENESIS Simulator, GEneral NEural SImulation System | 2026-08-12 10:49:24 | 459 | ||||||
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ChiCTR - Chinese Clinical Trial Registry Resource Report Resource Website 10+ mentions |
ChiCTR - Chinese Clinical Trial Registry (RRID:SCR_006037) | ChiCTR | service resource, data or information resource, database, clinical trial, data repository, storage service resource, registry | National clinical trial registry by Ministry of Health of China to join World Health Organization International Clinical Trial Registration Platform (WHO ICTRP Primary Registry), and the approved Primary Registry of WHO ICTRP. It registers both Chinese and global clinical trials, receives data from Partner Registers certified by the WHO ICTRP, and submits data to the WHO ICTRP Central Repository for global search. Moreover, based upon the talent and technical platform, consisting of Chinese Evidence-based Medicine Centre of Ministry of Health of China, Virtual Research Centre of Evidence-Based Medicine of Ministry of Education of China, Chinese Cochrane Centre, UK Cochrane Centre and International Clinical Epidemiology Network Resource and Training Centre in West China Hospital, Sichuan University (INCLEN CERTC), ChiCTR is responsible for providing consultations on trial design, central randomization service, guidance on the writing of clinical trial reports and relevant training. WHO takes the lead in establishing the global clinical trial registration system, which is agreed upon by governments from all over the world. There are both ethical and scientific reasons for clinical trial registration. Trial participants expect that their contributions to biomedical knowledge will be used to improve health care for everyone. Open access to information about ongoing and completed trials meets the ethical duty to trial participants, and promotes greater trust and public confidence in clinical research. Furthermore, trial registration ensures that the results of all trials can be tracked down and should help to reduce unnecessary duplication of research through greater awareness of existing trials and results. The mission of ChiCTR is to Unite clinicians, clinical epidemiologists, biostatisticians, epidemiologists and health care managers both at home and abroad, to manage clinical trials in a strict and scientific manner, and to promote their quality in China, so as to provide reliable evidences from clinical trials for health care workers, consumers and medical policy decision makers, and also to use medical resources more effectively to provide better service for Chinese people and all human beings. Any trial performed in human beings is considered as a clinical trial, and should be registered before its implementation. All the registered clinical trials will be granted a unique registration number by WHO ICTRP. | clinical trial, registry, registration, clinical, trial, china |
is related to: WHO International Clinical Trials Registry Platform has parent organization: Sichuan University; Sichuan; China |
nlx_151504 | SCR_006037 | Chinese Clinical Trial Registry | 2026-08-12 10:49:19 | 42 | ||||||||
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PatientCrossroads Resource Report Resource Website 1+ mentions |
PatientCrossroads (RRID:SCR_006279) | PatientCrossroads | portal, data or information resource, topical portal, people resource, patient registry | A trusted third-party gatekeeper of patient data from participants in a rare disease ecosystem, collecting and managing the information in a scalable, cost-effective manner. Each patient registry provides critical disease knowledge which makes that disease easier to study, increasing the probability a treatment can be developed. PatientCrossroads takes a network approach to patient registry programs. Unlike companies that merely sell registry software, we offer a full range of administration, management, and genetic curation services. What does this consolidated, patient-centric approach to patient registries mean? * Patients can more easily find registries and provide their valuable data (including locations of blood and tissue samples as well as reports of diagnoses, disease symptoms, treatment usage, and lifestyle activities) * Patients can be confident in the privacy of their de-identified data and the knowledge that PatientCrossroads does not sell patient data * Researchers and pharmaceutical companies have a larger, more easily accessible pool of potential patients for research studies and clinical trials targeting specific rare diseases * Pharmaceutical companies can collect post-market surveillance data in a more scalable and cost-effective manner * Rare disease advocacy and research foundations can more easily organize their global patient populations for inclusion in trials and studies | disease, treatment, clinical, patient, registry, drug discovery, clinical trial, research study, genetics, biorepository | is parent organization of: NF Registry | Rare disease | nlx_151889 | SCR_006279 | Patient Crossroads | 2026-08-12 10:49:25 | 3 | |||||||
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GOToolBox Functional Investigation of Gene Datasets Resource Report Resource Website 10+ mentions |
GOToolBox Functional Investigation of Gene Datasets (RRID:SCR_003192) | GOToolBox | service resource, software resource, source code | The GOToolBox web server provides a series of programs allowing the functional investigation of groups of genes, based on the Gene Ontology resource. The web version of the GOToolBox is free for non-commercial users only. Users from commercial companies are allowed to use the site during a reasonable testing period. For a regular use of the web version, a license fee should be paid. We have developed methods and tools based on the Gene Ontology (GO) resource allowing the identification of statistically over- or under-represented terms in a gene dataset; the clustering of functionally related genes within a set; and the retrieval of genes sharing annotations with a query gene. GO annotations can also be constrained to a slim hierarchy or a given level of the ontology. The source codes are available upon request, and distributed under the GPL license. Platform: Online tool | gene, annotation, statistical analysis, slimmer-type tool, function, cluster, gene association, gene ontology |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Center for Genomic Regulation; Barcelona; Spain |
Action Bioinformatique inter-EPST ; French Ministere de l'Education de la Recherche et de la Technologie ; Fondation pour la Recherche Medicale |
PMID:15575967 | Free, Freely available | nif-0000-30623 | http://burgundy.cmmt.ubc.ca/GOToolBox/ | SCR_003192 | GOToolBox - Functional Investigation of Gene Datasets, GOToolBox : Functional Investigation of Gene Datasets | 2026-08-12 10:48:45 | 35 | ||||
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AmphoraNet Resource Report Resource Website 10+ mentions |
AmphoraNet (RRID:SCR_005009) | AmphoraNet | production service resource, data analysis service, analysis service resource, service resource | Webserver implementation of the AMPHORA2 workflow for phylogenetic analysis of metagenomic shotgun sequencing data. It is capable of assigning a probability-weighted taxonomic group for each phylogenetic marker gene found in the input metagenomic sample. | dna sequence, amino acid sequence, dna, sequence, amino acid, phylogenetic, reliability score, nucleotide, protein, nucleotide sequence, protein sequence, phylogenetic analysis, metagenomic, metagenomics, phylotyping, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Eotvos Lorand University; Budapest; Hungary |
PMID:24144838 | Acknowledgement requested, Free, Public | biotools:amphoranet, OMICS_01450 | https://bio.tools/amphoranet | SCR_005009 | 2026-08-12 10:49:05 | 16 | ||||||
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Scholarly Open Access Resource Report Resource Website 10+ mentions |
Scholarly Open Access (RRID:SCR_002650) | Scholarly OA | data or information resource, narrative resource, blog | Blog featuring critical analysis of scholarly open-access journals by Jeffrey Beale. Good tool to consult if you have suspicions that a journal is less than legit. Jeffrey Beall works as a librarian at Auraria Library, University of Colorado Denver, in Denver, Colorado. | open access | is listed by: FORCE11 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156078 | SCR_002650 | 2026-08-12 10:48:38 | 12 | ||||||||
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SECISearch3 and Seblastian Resource Report Resource Website 1+ mentions |
SECISearch3 and Seblastian (RRID:SCR_003186) | SECISearch, Seblastian, SECISearch3 | production service resource, data analysis service, analysis service resource, service resource | Web server to predict eukaryotic selenoproteins and SECIS (SElenoCysteine Insertion Sequences) elements along nucleotide sequences. SECISearch3 replaces its predecessor SECISearch as a tool for prediction of eukaryotic SECIS elements. Seblastian is a method for selenoprotein gene detection that uses SECISearch3 and then predicts selenoprotein sequences encoded upstream of SECIS elements. Seblastian is able to both identify known selenoproteins and predict new selenoproteins. | selenoprotein, nucleotide sequence, selenocysteine insertion sequence, sequence |
is listed by: OMICtools has parent organization: Center for Genomic Regulation; Barcelona; Spain |
PMID:23783574 | Public, Acknowledgement requested | OMICS_01566 | SCR_003186 | Selenoprotein prediction server | 2026-08-12 10:48:45 | 1 | ||||||
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MLTreeMap Resource Report Resource Website 1+ mentions |
MLTreeMap (RRID:SCR_004792) | MLTreeMap | production service resource, data analysis service, analysis service resource, service resource | Data analysis service that analyzes DNA sequences and determines their most likely phylogenetic origin. Its main use is in metagenomics projects, where DNA is isolated directly from natural environments and sequenced (the organisms from which the DNA originates are often entirely undescribed). It will search such sequences for suitable marker genes, and will use maximum likelihood analysis to place them in the ''''Tree of Life''''. This placement is more reliable than simply assessing the closest relative of a sequence using BLAST. More importantly, MLTreeMap decides not only who is the closest relative of your query sequence, but also how deep in the tree of life it probably branched off. Additionally, MLTreeMap searches the sequences for genes, which are coding for key enzymes of important functional pathways, such as RuBisCo, methane monooxygenase or nitrogenase. In case of a positive hit, MLTreeMap uses maximum likelihood analysis to place them in the respective ''''gene-family tree''''. | phylogeny, gene, fasta, dna sequence, nucleotide sequence, metagenomics, metagenome, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: COG has parent organization: University of Zurich; Zurich; Switzerland |
PMID:20687950 | biotools:mltreemap, OMICS_01457 | https://bio.tools/mltreemap | SCR_004792 | Phylogenetic analysis of metagenomics sequence data | 2026-08-12 10:49:02 | 4 | ||||||
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Identifiers.org Resource Report Resource Website 50+ mentions |
Identifiers.org (RRID:SCR_003735) | Identifiers.org | production service resource, identifier resolution, service resource | A system providing resolvable persistent Uniform Resource Identifiers (URIs) used to identify data for the scientific community, with a current focus on the Life Sciences domain. The provision of resolvable identifiers (URLs) fits well with the Semantic Web vision, and the Linked Data initiative. It provides direct access to the identified data using one chosen physical location (or resource). If more than one physical locations providing the data are recorded in the Registry, then you can access them via the top banner or by using a profile. | identifier, life sciences, bio.tools |
uses: MIRIAM Resources is listed by: bio.tools is listed by: Debian has parent organization: European Bioinformatics Institute |
Free | nlx_157931, biotools:identifiers.org | https://bio.tools/identifiers.org | SCR_003735 | 2026-08-12 10:48:51 | 59 | |||||||
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bioPIXIE Resource Report Resource Website 1+ mentions |
bioPIXIE (RRID:SCR_004182) | bioPIXIE | production service resource, data analysis service, analysis service resource, service resource | bioPIXIE is a general system for discovery of biological networks through integration of diverse genome-wide functional data. This novel system for biological data integration and visualization, allows you to discover interaction networks and pathways in which your gene(s) (e.g. BNI1, YFL039C) of interest participate. The system is based on a Bayesian algorithm for identification of biological networks based on integrated diverse genomic data. To start using bioPIXIE, enter your genes of interest into the search box. You can use ORF names or aliases. If you enter multiple genes, they can be separated by commas or returns. Press ''submit''. bioPIXIE uses a probabilistic Bayesian algorithm to identify genes that are most likely to be in the same pathway/functional neighborhood as your genes of interest. It then displays biological network for the resulting genes as a graph. The nodes in the graph are genes (clicking on each node will bring up SGD page for that gene) and edges are interactions (clicking on each edge will show evidence used to predict this interaction). Most likely, the first results to load on the results page will be a list of significant Gene Ontology terms. This list is calculated for the genes in the biological network created by the bioPIXIE algorithm. If a gene ontology term appears on this list with a low p-value, it is statistically significantly overrepresented in this biological network. As you move the mouse over genes in the network, interactions involving these genes are highlighted. If you click on any of the highlighted interactions graph, evidence pop-up window will appear. The Evidence pop-up lists all evidence for this interaction, with links to the papers that produced this evidence - clicking these links will bring up the relevant source citation(s) in PubMed. You may need to download the Adobe Scalable Vector Graphic (SVG) plugin to utilize the visualization tool (you will be prompted if you need it). | prediction, bayesian network, probabilistic, interaction, network | has parent organization: Princeton University; New Jersey; USA | NHGRI T32 HG003284; NIGMS R01 GM071966; NHGRI R01 HG003471; NIGMS P50 GM071508; NSF DGE-9972930; NSF IIS-0513552 |
PMID:16420673 | nlx_20893 | SCR_004182 | biological Process Inference from eXperimental Interaction Evidence | 2026-08-12 10:48:56 | 1 | ||||||
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Primer-BLAST Resource Report Resource Website 5000+ mentions |
Primer-BLAST (RRID:SCR_003095) | Primer-BLAST | production service resource, data analysis service, analysis service resource, service resource | A tool to design target-specific primers for polymerase chain reaction (PCR). It uses Primer3 to design PCR primers and then uses BLAST and global alignment algorithm to screen primers against user-selected database in order to avoid primer pairs (all combinations including forward-reverse primer pair, forward-forward as well as reverse-reverse pairs) that can cause non-specific amplifications. | primer, blast, pcr target, polymerase chain reaction, primer design |
is listed by: OMICtools is listed by: SoftCite is related to: Primer3 has parent organization: NCBI |
PMID:22708584 | Free, Freely available | OMICS_02343 | SCR_003095 | 2026-08-12 10:48:44 | 6113 | |||||||
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SHEsis: Analysis Tools For Random Samples Resource Report Resource Website 50+ mentions |
SHEsis: Analysis Tools For Random Samples (RRID:SCR_002958) | SHEsis | production service resource, data analysis service, analysis service resource, service resource | A powerful web-based platform for analyses of linkage disequilibrium, haplotype construction, and genetic association at polymorphism loci. | analysis, disequilibrium, haplotype, genetic, association, polymorphism, locus, linkage disequilibrium | has parent organization: Shanghai Jiao Tong University; Shanghai; China | Major State Basic Research Development program of China ; National High Technology Research and Development Program of China |
PMID:19290020 PMID:15740637 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30105 | http://analysis.bio-x.cn/myAnalysis.php | SCR_002958 | 2026-08-12 10:48:42 | 82 | |||||
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siDirect Resource Report Resource Website 100+ mentions |
siDirect (RRID:SCR_004853) | production service resource, data analysis service, analysis service resource, service resource | siDirect 2.0 provides functional and off-target minimized siRNA design for mammalian RNAi. The previous version of our software designed functional siRNAs by considering the relationship between siRNA sequence and RNAi activity, and provided them along with the enumeration of potential off-target gene candidates by using a fast and sensitive homology search algorithm. In the new version, the siRNA design algorithm is extensively updated to eliminate off-target effects by reflecting our recent finding that the capability of siRNA to induce off-target effect is highly correlated to the thermodynamic stability, or the melting temperature (Tm), of the seed-target duplex, which is formed between the nucleotides positioned at 2-8 from the 5'' end of the siRNA guide strand and its target mRNA. Selection of siRNAs with lower seed-target duplex stabilities (benchmark Tm < 21.5 degrees C) followed by the elimination of unrelated transcripts with nearly perfect match should minimize the off-target effects. siDirect 2.0 provides functional, target-specific siRNA design with the updated algorithm which significantly reduces off-target silencing. When the candidate functional siRNAs could form seed-target duplexes with Tm values below 21.5 degrees C, and their 19-nt regions spanning positions 2-20 of both strands have at least two mismatches to any other non-targeted transcripts, siDirect 2.0 can design at least one qualified siRNA for > 94% of human mRNA sequences in RefSeq. Enter an accession number and retrieve sequence or Paste in a nucleotide sequence. | has parent organization: University of Tokyo; Tokyo; Japan | Special Coordination Fund for Promoting Science and Technology ; Ministry of Education Culture Sports Science and Technology of Japan ; Grant-in-Aid for Scientific Research on Priority Areas 12208003 |
PMID:19948054 PMID:15215364 |
nlx_83672 | SCR_004853 | 2026-08-12 10:49:03 | 294 | |||||||||
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AllerHunter: Cross-reactive Allergen Prediction Home Resource Report Resource Website 10+ mentions |
AllerHunter: Cross-reactive Allergen Prediction Home (RRID:SCR_002950) | AllerHunter | production service resource, data analysis service, analysis service resource, service resource | A cross-reactive allergen prediction program built on a combination of Support Vector Machine (SVM) and pairwise sequence similarity. Cross-reactivity is based on similarity of proteins to allergens. However, not all proteins with similar sequence or structure to known allergens are cross-reactive allergens. AllerHunter aims to predict allergens and non-allergens with high sensitivity and specificity, without compromising efficiency at classification of proteins with similar sequence to known allergens. There are distinct differences between prediction of allergenicity and cross-reactivity of allergens. Allergenicity is the immunogenic potential of an allergen to induce IgE antibody production, whereas cross-reactivity is the potential of a substance to bind to IgE previously induced by a known allergen. It is difficult to predict allergenicity because causes of immunogenicity of allergens are still not completely clear. However it is possible to predict cross-reactivity since it implies similarity in IgE binding sites. Please provide protein sequence in fasta format. | fasta, allergen, prediction program, support vector machine | has parent organization: National University of Singapore; Singapore; Singapore | PMID:19516900 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30082 | SCR_002950 | AllerHunter: Cross-reactive Allergen Prediction Program | 2026-08-12 10:48:42 | 12 | ||||||
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ProFunc Resource Report Resource Website 50+ mentions |
ProFunc (RRID:SCR_004450) | ProFunc | production service resource, data analysis service, analysis service resource, service resource | The ProFunc server had been developed to help identify the likely biochemical function of a protein from its three-dimensional structure. It uses both sequence- and structure-based methods including fold matching, residue conservation, surface cleft analysis, and functional 3D templates, to identify both the protein''''s likely active site and possible homologues in the PDB. Often, where one method fails to provide any functional insight another may be more helpful. You can submit your own structure, analyze an existing PDB entry, or retrieve the results of a previously submitted run. The files are usually stored for about 6 months before being deleted. However, they are stored on a partition that is not backed up; so, in principle, they could disappear at any time. | gold standard |
is related to: PDBsum has parent organization: European Bioinformatics Institute |
DOE contract W-31-109-Eng-38; NIGMS GM62414; European Union FP6 contract LHSG-CT-2003-503265 |
PMID:15980588 PMID:16019027 |
nlx_44430 | SCR_004450 | ProFunc - prediction of protein function from 3D structure, ProFunc: Analysis of a protein''''s 3D structure to help identify its likely biochemical function | 2026-08-12 10:48:59 | 72 | ||||||
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MAGI Resource Report Resource Website 10+ mentions |
MAGI (RRID:SCR_003360) | production service resource, data analysis service, analysis service resource, service resource | A web service for fast microRNA-Seq data analysis in a GPU infrastructure. | fastq, c, perl, php, software program, gpu/cuda |
is listed by: OMICtools has parent organization: University of California at San Diego; California; USA |
PMID:24907367 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_04636 | SCR_003360 | 2026-08-12 10:48:47 | 30 | ||||||||
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INMEX Resource Report Resource Website 10+ mentions |
INMEX (RRID:SCR_004173) | INMEX | production service resource, data analysis service, analysis service resource, service resource | A web-based tool to support meta-analysis of multiple gene-expression data sets, as well as to enable integration of data sets from gene expression and metabolomics experiments. INMEX contains three functional modules. The data preparation module supports flexible data processing, annotation and visualization of individual data sets. The statistical analysis module allows researchers to combine multiple data sets based on P-values, effect sizes, rank orders and other features. The significant genes can be examined in functional analysis module for enriched Gene Ontology terms or Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, or expression profile visualization. INMEX has built-in support for common gene/metabolite identifiers (IDs), as well as 45 popular microarray platforms for human, mouse and rat. Complex operations are performed through a user-friendly web interface in a step-by-step manner. | gene expression, meta-analysis, metabolomics, pathway, gene, metabolite, visualization, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology is related to: KEGG is related to: Human Metabolome Database has parent organization: University of British Columbia; British Columbia; Canada |
Killam Trust ; Canadian Institutes of Health Research |
PMID:23766290 | Acknowledgement requested | biotools:inmex, OMICS_01546 | https://bio.tools/inmex | SCR_004173 | INtegrative Meta-analysis of EXpression data, INMEX - INtegrative Meta-analysis of EXpression data | 2026-08-12 10:48:56 | 19 |
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