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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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WegoLoc Resource Report Resource Website 1+ mentions |
WegoLoc (RRID:SCR_001402) | WegoLoc | production service resource, data analysis service, analysis service resource, service resource | Data analysis service that predicts protein subcellular localizations of animal, fungal, plant, and human proteins based on sequence similarity and gene ontology information. | subcellular localization, protein |
is listed by: OMICtools is related to: Gene Ontology |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01636 | SCR_001402 | weighted gene ontology term based subcellular locallization prediction | 2026-08-12 10:48:23 | 4 | |||||||
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ERGO Resource Report Resource Website 50+ mentions |
ERGO (RRID:SCR_001243) | ERGO | production service resource, data analysis service, analysis service resource, service resource | A web-based genome analysis platform that integrates proprietary functional genomic data, metabolic reconstructions, expression profiling, and biochemical and microbiological data with publicly available information. Focused on microbial genomics, it provides better and faster identification of gene function across all organisms. Building upon a comprehensive genomic database integrated with a collection of microbial metabolic and non-metabolic pathways and using proprietary algorithms, it assigns functions to genes, integrates genes into pathways, and identifies previously unknown or mischaracterized genes, cryptic pathways and gene products. . * Automated and manual annotation of genes and genomes * Analysis of metabolic and non-metabolic pathways to understand organism physiology * Comparison of multiple genomes to identify shared and unique features and SNPs * Functional analysis of gene expression microarray data * Data-mining for target gene discovery * In silico metabolic engineering and strain improvement | genome analysis, genome, annotation, database, software, comparative genomics, function, gene, pathway, gene expression, microarray, FASEB list | is listed by: OMICtools | Restricted | OMICS_02097 | SCR_001243 | ERGO Genome Analysis and Discovery System, ERGO Genome Analysis & Discovery System | 2026-08-12 10:48:21 | 68 | |||||||
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Penn Community Outreach Using Health System Informatics Core Resource Report Resource Website 1+ mentions |
Penn Community Outreach Using Health System Informatics Core (RRID:SCR_000304) | COHSI | data or information resource, portal, organization portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. Informatics core for the purpose of promoting clinical research by collecting data from the Penn Health System. | informatics, community development, awareness, clinical research |
is listed by: Eagle I has parent organization: University of Pennsylvania; Philadelphia; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156476 | http://eagle-i.itmat.upenn.edu/i/00000141-93f7-4d80-91c7-0c6080000000 | SCR_000304 | Penn COHSI | 2026-08-12 10:48:12 | 1 | ||||||
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psignifit Resource Report Resource Website 1+ mentions |
psignifit (RRID:SCR_024196) | software library, software toolkit, software resource | Software toolbox to fit psychometric functions and to test hypotheses about psychometric data. | fit psychometric functions, test hypotheses, psychometric data, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/psignifit/ | SCR_024196 | 2026-08-12 10:53:01 | 3 | |||||||||
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sumaclust Resource Report Resource Website 1+ mentions |
sumaclust (RRID:SCR_024352) | software library, software toolkit, software resource | Software tool aims to cluster sequences in a way that is fast and exact at the same time. | cluster sequences, fast and exact clustering, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_19112 | https://sources.debian.org/src/sumaclust/ | SCR_024352 | 2026-08-12 10:53:06 | 2 | ||||||||
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Inference of CRISPR Edits Resource Report Resource Website 100+ mentions |
Inference of CRISPR Edits (RRID:SCR_024508) | ICE | production service resource, software resource, analysis service resource, service resource | Software tool that offers analysis of CRISPR editing data. Used for inference of CRISPR edits from Sanger trace data. | analysis of CRISPR editing data, CRISPR editing analysis, | is listed by: SoftCite | PMID:35119294 | Free, Freely available | https://github.com/synthego-open/ice#ref2 | SCR_024508 | Synthego Inference of CRISPR Edits | 2026-08-12 10:53:15 | 103 | ||||||
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ODIN Resource Report Resource Website 10+ mentions |
ODIN (RRID:SCR_001386) | ODIN | service resource, software resource, source code | Service (Beta) that allows users to search the DataCite Metadata Store, and add their research outputs including datasets, software, and others to their ORCID profile. This should increase the visibility of these research data, and will make it easier to use these data citations in applications that connect to the ORCID Registry. In addition, the service is also providing formatted citations in several popular citation styles, supports COinS, links to related resources, and displays the attached Creative Commons license where this information is available. The DataCite Metadata Store of course also contains many text documents from academic publishers and services such as figshare or PeerJ Preprints, and these works can also be claimed. This tool is a collaborative effort by ORCID, CrossRef and DataCite. | data citation, scholarly communication, interoperability, access, discovery, sustainability, digital object identifier |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: ORCID - Open Researcher and Contributor ID has parent organization: DataCite |
European Union FP7 Coordination and Support Action 312788 | Unless otherwise noted, Creative Commons Attribution License, Account required | nlx_152557 | http://www.nitrc.org/projects/od1n http://github.com/mfenner/cr-search | SCR_001386 | ORCID and DataCite Interoperability Network | 2026-08-12 10:48:23 | 31 | |||||
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Schizophrenia and Bipolar Disorder Genetics Blog Resource Report Resource Website 1+ mentions |
Schizophrenia and Bipolar Disorder Genetics Blog (RRID:SCR_001541) | data or information resource, narrative resource, blog | This resource aims to provide information for the general public on the background and current progress of scientific research into the role of genetics in these disorders. Additionally, it also aims to provide a forum for the discussion of aspects of psychiatric genetics open to members of the research community. | genetics, disorder, psychiatric, research, scientific | has parent organization: University of Edinburgh; Scotland; United Kingdom | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10419 | SCR_001541 | Genetics Blog | 2026-08-12 10:48:25 | 2 | ||||||||
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Sumatra Resource Report Resource Website 10+ mentions |
Sumatra (RRID:SCR_001381) | electronic laboratory notebook, software resource, software application | A software tool for managing and tracking projects based on numerical simulation or analysis to support reproducible research. It can be thought of as an automated electronic lab notebook for simulation/analysis projects. Sumatra consists of: a command-line interface, smt, for launching simulations/analyses with automatic recording of information about the context, annotating these records, linking to data files, etc.; a web interface with a built-in web-server, smtweb, for browsing and annotating simulation/analysis results; a LaTeX package and Sphinx extension for including Sumatra-tracked figures and links to provenance information in papers and other documents; and a Python API, on which smt and smtweb are based, that can be used in personalized scripts in place of using smt. | simulation, analysis, python, numerical simulation, manage, track |
uses: Python Programming Language is listed by: INCF Software Center has parent organization: NeuralEnsemble |
Free, Freely Available | nlx_152549 | SCR_001381 | Sumatra: automated tracking of scientific computations | 2026-08-12 10:48:23 | 27 | ||||||||
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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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