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http://flytrap.med.yale.edu/

The FlyTrap database presents the current results of large scale protein trapping screens that provide both information on which cells express each tagged gene, and subcellular localization of GFP-tagged proteins. Expression is under the control of endogenous promoter and enhancer elements, allowing for visualization of normal expression patterns. Drosophila proteins tagged with Green Fluorescent Protein (GFP) were created by insertion into genes of an artificial exon encoding GFP flanked by splice acceptor (SA) and splice donor (SD) sequences so that expression of GFP relies on splicing into mature mRNAs and in-frame fusion.

Proper citation: FlyTrap- GFP Protein Trap Database (RRID:SCR_013354) Copy   

•   Source: SciCrunch Registry

http://thenode.biologists.com/

The Node: a community site for development biologists

Proper citation: The Node (RRID:SCR_013071) Copy   

•   Source: SciCrunch Registry

http://www.collectf.org/browse/home/

A database of experimentally-validate transcription factor binding sites (TFBS) in the Bacteria domain. CollecTF places special emphasis on providing a curation process that captures the experimental support for sites as reported by authors in peer-reviewed publications. Reported binding sites are mapped to NCBI RefSeq complete genome records. The database can be browsed by transcription factor families, NCBI taxonomy or experimental support, or through customized searches integrating these three elements.

Proper citation: CollecTF (RRID:SCR_014405) Copy   

•   Source: SciCrunch Registry

http://www.neurofly.de

An on-going atlas project of the Virtual Insect Brain Project with the goal of reconstructing and standardizing Gal4 expression patterns in Drosophila brains. Neurofly will be a web-based tool that will enable the online comparison of mutations and Gal4 expression patterns in the Drosophila brain. To this end, a database of reconstructed and standardized Gal4 expression patterns - on the basis of the existing Drosophila StandardBrain - was developed along with tools for 3D image data set processing. Users will be able to evaluate the expression patterns intersections of various Gal4 driver lines and/or mutations.

Proper citation: Neurofly (RRID:SCR_013833) Copy   

•   Source: SciCrunch Registry

http://www.glycoepitope.jp

A database of carbohydrate antigens and matching antibodies. Epitopes and antibodies are listed within the database. Users may also search for epitopes and antibodies by keyword, epitope ID, tissue, receptor, enzyme, and other fields.

Proper citation: GlycoEpitope (RRID:SCR_014404) Copy   

•   Source: SciCrunch Registry

http://unicarb-db.biomedicine.gu.se

An experimental glycomic MS database initially created to meet the in-house need to store structural and MS-glycomic data. Users can search by taxonomy and tissue, mass and composition, and MS/MS.

Proper citation: UniCarb-DB (RRID:SCR_014407) Copy   

•   Source: SciCrunch Registry

http://proline.bic.nus.edu.sg/dedb/

Database on Drosophila melanogaster exons presented in a splicing graph form. Data is based on release 3.2 of the Drosophila melanogaster genome annotations available at FlyBase. The gene structure information extracted from the annotations were checked, clustered and transformed into splicing graph. The splicing graph form of the gene constructs were then used for classification of the various types of alternative splicing events. In addition, Pfam domains were mapped onto the gene structure. Users can query the database using the query page using BLAST, FlyBase Gene Name, FlyBase Gene Symbol, Pfam Accession Number and Pfam Identifier. This allows users to determine the Drosophila melanogaster homology of their gene using a BLAST search and to visualize the alternative splicing variants if any. Users can also determine genes containing a particular domain using the Pfam Accession Numbers and Identifiers.

Proper citation: Drosophila melanogaster Exon Database (RRID:SCR_013441) Copy   

•   Source: SciCrunch Registry

http://www.niddk.nih.gov/research-funding/research-resources/Pages/default.aspx

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 29,2023. Registry listing NIDDK resources, such as reagents, data, and protocols. They are derived from publicly available information provided by NIDDK-funded investigators, projects, and publications.

Proper citation: NIDDK Research Resources (RRID:SCR_014372) Copy   

•   Source: SciCrunch Registry

http://www.psychotropics.dk/

The Lundbeck Institute is pleased to present Psychotropics Online, a comprehensive guide to CNS compounds and products. A database of psychotropic and neurological drugs. Generic name, Trade name, Description, Code numbers, Monographies, Tranquilizers - Anxiolytics, Anxiolytics / Antipsychotics, Neuroleptics and Antipsychotics, Monoamine Oxidase Inhibitors, Antidepressants, Antidementia drugs, Sympathomimetics, Antiparkinsonians, Anticonvulsants, Hallucinogenic Agents, Additional Group, Biochemical profiles, Side-effects, Antipsychotics, Tranquilizers - anxiolytics, Tricyclic Antidepressants (TCAs), Selective Serotonin Reuptake Inhibitors (SSRIs), Selective Serotonin and Noradrenaline Reuptake Inhibitors (SNRIs), Selective Noradrenaline Reuptake Inhibitors (NARIs), MAO inhibitors (MAOIs), Sympathomimetics, Anticonvulsants, Lithium, Barbiturates, Street names, Terminal plasma half-lives, Orphan drugs

Proper citation: Psychotropics (RRID:SCR_013600) Copy   

•   Source: SciCrunch Registry

http://spd.cbi.pku.edu.cn

A collection of secreted proteins from Human, Mouse and Rat proteomes, which includes sequences from SwissProt, Trembl, Ensembl and Refseq. The 18,152 entries are classified into fourteen functional categories, including "apolipoprotein", "cytokine", "protease", "toxin", etc. To make the dataset more comprehensive, nine related datasets were also collected, such as SPDI, Riken mouse secretome, SwissProt vertebrate secreted proteins, SubLoc etc.

Proper citation: Secreted Protein Database (RRID:SCR_013448) Copy   

•   Source: SciCrunch Registry

http://www.papercritic.com

A database that archives publications and allows users to review and critique them. Users can write comments for and rate submitted publications for references, originality, argumentation, and reliability. Papercritic also collects tweets and blog posts about published papers to add as reviews and comments. Researchers who submit their published work to PaperCritic can keep track of multiple types of feedback. All reviews must be submitted with full identity disclosure.

Proper citation: Paper Critic (RRID:SCR_014019) Copy   

•   Source: SciCrunch Registry

http://bacillus.genome.jp/

This website provides a resource for the Bacillus subtilis genome. It provides a list of mutants, DNA array data, and search features against both the whole genome and coding sequences. It also contains Kegarrays and access to the KEGG Expression Database.

Proper citation: BSORF - Bacillus Subtilis Genome Database (RRID:SCR_013451) Copy   

•   Source: SciCrunch Registry

http://toxodb.org/toxo/

A genome and functional genomic database for the protozoan parasite Toxoplasma gondii. It incorporates the sequence and annotation of the T. gondii ME49 strain, as well as genome sequences for the GT1, VEG and RH (Chr Ia, Chr Ib) strains. Sequence information is integrated with various other genomic-scale data, including community annotation, ESTs, gene expression and proteomics data. Organisms * Toxoplasma gondii (ME49, RH, GT1, Veg strains) * Neospora caninum * environmental isolate sequences from numerous species Tools * BLAST: Identify Sequence Similarities * Sequence Retrieval: Retrieve Specific Sequences using IDs and coordinates * PubMed and Entrez: View the Latest Toxoplasma, Neospora Pubmed and Entrez Results * Genome Browser: View Sequences and Features in the genome browser * Ancillary Genome Browse: Access Additional info like Probeset data and Toxoplasma Array info

Proper citation: ApiDB ToxoDB (RRID:SCR_013453) Copy   

•   Source: SciCrunch Registry

http://findingsapp.com

An ELN (electronic lab notebook) software application that allows researchers to organize and manage experiment tasks, protocols, and results. Users can divide experiments into tasks spread across weeks and keep track of multiple experiments and protocols using a variety of apps, such as timestamps and completion markers. Files can be stored in the Findings library and opened in a given application.

Proper citation: Findings App (RRID:SCR_013972) Copy   

•   Source: SciCrunch Registry

http://animaldiversity.ummz.umich.edu/site/index.html

Animal Diversity Web (ADW) is an online database of animal natural history, distribution, classification, and conservation biology at the University of Michigan :Animal Diversity Web Has: Thousands of species accounts about individual animal species. These may include text, pictures of living animals, photographs and movies of specimens, and/or recordings of sounds. Students write the text of these accounts and we cannot guarantee their accuracy. Descriptions of levels of organization above the species level, especially phyla, classes, and in some cases, orders and families. Hundreds of hyperlinked pages and images illustrate the traits and general biology of these groups. Professional biologists prepare this part. :Animal Diversity Web Is An Online Encyclopedia: ADW is a large searchable encyclopedia of the natural history of animals. Every day, thousands of classroom students and informal visitors use it to answer animal questions. Other sites specialize in local, endangered, or particular kinds of animals. We aim to be as comprehensive as possible. :A Science Learning Tool: ADW facilitates inquiry-driven learning, that is, teaching about science by leading students to use the methods of science. Our large database is structured, providing consistent information for all species to foster comparisons. An advanced search tool allows a user to call up species accounts fitting any combination of descriptors. Students can explore for patterns and relationships, learn how to frame and answer scientific questions and, with the help of a good teacher, experience the excitement and satisfaction of doing science. Our long-term goal is to create a database rich enough that students can discover for themselves basic concepts in ecology and conservation biology. :A Virtual Museum: ADW provides a way to make the contents of research museums available globally for teaching and research. So far, our efforts have been directed mainly at mammals. Photographs of scientific specimens are available for representative species from most mammal families. We''ve also included several hundred Quick Time Virtual Reality Movies of skulls. These allow the user to rotate the specimen, providing an excellent impression of its 3-dimensional structure. We''ve written in depth about and illustrated many of the characteristics of interest to students of mammals. An important goal for the future is to expand to cover other groups of animals and include other media such as animal behavior video. :Wiki features, database, teaching tool :

Proper citation: Animal Diversity Web (RRID:SCR_013658) Copy   

•   Source: SciCrunch Registry

http://www.sherpa.ac.uk/romeo/index.php?la=en&fIDnum=/&mode=simple

A database which houses publisher policies regarding the self- archiving of journal articles on the web and in Open Access repositories. RoMEO contains publishers' general policies on self-archiving of journal articles and certain conference series. Each entry provides a summary of the publisher's policy, including what version of an article can be deposited, where it can be deposited, and any conditions that are attached to that deposit.

Proper citation: SHERPA RoMEO (RRID:SCR_013815) Copy   

•   Source: SciCrunch Registry

http://msub.csbio.unc.edu/

A custom genome browser which provides detailed answers to questions on the haplotype diversity and phylogenetic origin of the genetic variation underlying any genomic region of most laboratory strains of mice (both classical and wild-derived). Users can select a region of the genome and a set of laboratory strains and/or wild caught mice. The region is selected by specifying the start (e.g. 31200000 or 31200K or 31.2M), and end of the interval and the chromosome (i.e, autosome number and X chromosome). Samples can be selected by name or by entire set. Data sets include information on subspecific origin, heterozygosity regions, and haplotype coloring, among others.

Proper citation: Mouse Phylogeny Viewer (RRID:SCR_014071) Copy   

•   Source: SciCrunch Registry

https://www.nanomaterialregistry.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 9,2023. Registry that archives curated nanomaterial research data and their biological and environmental implications. The Registry provides data management plans for researchers, and accepts users' public-ready data, archive them, integrate them into the registry, allowing for the data to be shared publicly. Users can request more information on specific nanomaterial records, compare multiple nanomaterials, and export data to their desktop.

Proper citation: Nanomaterial Registry (RRID:SCR_013700) Copy   

•   Source: SciCrunch Registry

https://scitran.github.io/

Scientific Transparency (SciTran) is a software project that has grown out of the Project on Scientific Transparency at Stanford University. At the heart of SciTran is a scientific data management system – SDM – designed to enable and foster reproducible research. SciTran SDM delivers efficient and robust archiving, organization, and sharing of scientific data. We have developed the system around neuroimaging data, but our goal is to build a system that is flexible enough to accomodate all types of scientific data – from paper-and-pencil tests to genomics data. SDM will also allow for the sharing of data and computations between remote sites. SciTran is open-source software, released under the MIT license. Our code is hosted on GitHub. Feel free to try it out or to contribute. Commercial support for SciTran SDM is available through our partners at Flywheel. Check out their demo, if you''d like to give SDM a quick try.

Proper citation: SciTran (RRID:SCR_013666) Copy   

•   Source: SciCrunch Registry

http://srv00.recas.ba.infn.it/py_script/REDIdb/overview.html

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 19, 2016. A relational database in which all editing information such as substitutions, insertions and deletions occurring in a wide range of organisms is stored and maintained in ad hoc designed textual flat files. Individual genes of interest can be searched by appropriate query strings containing the gene name or the intracellular location or the molecular type (as tRNA, rRNA, intron) or the organism or a combination of the previous terms. Moreover, each record of the REDIdb database can be also retrieved according to its specific accession number (more help on how to perform a REDIdb search is available at the ?help? page). To make easier the browsing of each REDIdb entry and quicker the identification of editing sites, two alternative but complementary facilities have been provided either to graphically display genomic and cDNA sequences or to show the corresponding alignment. In both cases, all editing sites are highlighted in colour and their relative positions are shown by mousing over.

Proper citation: REDIdb- RNA Editing Database (RRID:SCR_013429) Copy   

•   Source: SciCrunch Registry