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http://www.nordgen.org/index.php/en/content/view/full/467

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 18,2023.

Proper citation: Nordic Genetic Resource Centre (Plants) (RRID:SCR_010529) Copy   

•   Source: SciCrunch Registry

http://www.arabidopsisreactome.org

Curated database of core pathways and reactions in plant biology that covers biological pathways ranging from the basic processes of metabolism to high-level processes such as cell cycle regulation. While it is targeted at Arabidopsis pathways, it also includes many biological events from other plant species. This makes the database relevant to the large number of researchers who work on other plants. Arabidopsis Reactome currently contains both in-house curated pathways as well as imported pathways from AraCyc and KEGG databases. All the curated information is backed up by its provenance: either a literature citation or an electronic inference based on sequence similarity. Their ontology ensures that the various events are linked in an appropriate spatial and temporal context.

Proper citation: Arabidopsis Reactome (RRID:SCR_002063) Copy   

•   Source: SciCrunch Registry

http://www.phi-base.org/

Database that catalogs experimentally verified pathogenicity, virulence and effector genes from fungal, Oomycete and bacterial pathogens, which infect animal, plant, fungal and insect hosts. It is an invaluable resource in the discovery of genes in medically and agronomically important pathogens, which may be potential targets for chemical intervention. In collaboration with the FRAC team, it also includes antifungal compounds and their target genes. Each entry is curated by domain experts and is supported by strong experimental evidence (gene disruption experiments, STM etc), as well as literature references in which the original experiments are described. Each gene is presented with its nucleotide and deduced amino acid sequence, as well as a detailed description of the predicted protein's function during the host infection process. To facilitate data interoperability, genes have been annotated using controlled vocabularies and links to external sources (Gene Ontology terms, EC Numbers, NCBI taxonomy, EMBL, PubMed and FRAC).

Proper citation: PHI-base (RRID:SCR_003331) Copy   

•   Source: SciCrunch Registry

http://solgenomics.net/

A clade oriented, community curated database containing genomic, genetic, phenotypic and taxonomic information for plant genomes. Genomic information is presented in a comparative format and tied to important plant model species such as Arabidopsis. SGN provides tools such as: BLAST searches, the SolCyc biochemical pathways database, a CAPS experiment designer, an intron detection tool, an advanced Alignment Analyzer, and a browser for phylogenetic trees. The SGN code and database are developed as an open source project, and is based on database schemas developed by the GMOD project and SGN-specific extensions.

Proper citation: SGN (RRID:SCR_004933) Copy   

•   Source: SciCrunch Registry

http://www.ala.org.au/

Online repository of information about Australian plants, animals, and fungi. Development started in 2006. The Commonwealth Scientific and Industrial Research Organisation is organisation significantly involved in development of ALA.

Proper citation: Atlas of Living Australia (RRID:SCR_006467) Copy   

•   Source: SciCrunch Registry

http://gbrowse.org/

A database and interactive web site for manipulating and displaying annotations on genomes. Features include: detailed views of the genome; use of a variety of premade or personally made glyphs ; customizable order and appearance of tracks by administrators and end-users; search by annotation ID, name, or comment; support of third party annotation using GFF formats; DNA and GFF dumps; connectivity to different databases, including BioSQL and Chado; and a customizable plug-in architecture (e.g. run BLAST, find oligonucleotides, design primers, etc.). GBrowse is distributed as source code for Macintosh OS X, UNIX and Linux platforms, and as pre-packaged binaries for Windows machines. It can be installed using the standard Perl module build procedure, or automated using a network-based install script. In order to use the net installer, you will need to have Perl 5.8.6 or higher and the Apache web server installed. The wiki portion accepts data submissions.

Proper citation: GBrowse (RRID:SCR_006829) Copy   

•   Source: SciCrunch Registry

https://plantcyc.org/content/plantcyc-15.2.0

Multi species reference database. Comprehensive plant biochemical pathway database, containing curated information from literature and computational analyses about genes, enzymes, compounds, reactions, and pathways involved in primary and secondary metabolism.

Proper citation: PlantCyc (RRID:SCR_002110) Copy   

•   Source: SciCrunch Registry

http://www.lfd.uci.edu/

Biomedical technology research center and training resource that develops novel fluorescence technologies, including instrumentation, methods and software applicable to cellular imaging and the elucidation of dynamic processes in cells. The LFD's main activities are: * Services and Resources: the LFD provides a state-of-the-art laboratory for fluorescence measurements, microscopy and spectroscopy, with technical assistance to visiting scientists. * Research and Development: the LFD designs, tests, and implements advances in the technology of hardware, software, and biomedical applications. * Training and Dissemination: the LFD disseminates knowledge of fluorescence spectroscopic principles, instrumentation, and applications to the scientific community.

Proper citation: Laboratory for Fluorescence Dynamics (RRID:SCR_001437) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.psb.ugent.be/webtools/tapir/

Web server designed for prediction of plant microRNA targets.

Proper citation: TAPIR: target prediction for plant microRNAs (RRID:SCR_000237) Copy   

•   Source: SciCrunch Registry

https://github.com/hangelwen/miR-PREFeR

An accurate, fast, and easy-to-use plant miRNA prediction software tool using small RNA-Seq data. It utilizes expression patterns of miRNA and follows the criteria for plant microRNA annotation to accurately predict plant miRNAs from one or more small RNA-Seq data samples of the same species.

Proper citation: miR-PREFeR (RRID:SCR_003353) Copy   

•   Source: SciCrunch Registry

http://www.cropscience.bayer.com/

Crop science company with products in crop protection and nonagricultural pest control. It also has activities in seeds and plant traits. (Adapted from Wikipedia)

Proper citation: Bayer CropScience (RRID:SCR_010498) Copy   

•   Source: SciCrunch Registry

http://www3a.biotec.or.th/c-mii/

A software tool for plant miRNA and target identification. C-mii pipelines are based on combined steps and criteria from previous studies and also incorporated with several tools such as standalone BLAST and UNAFold and pre-installed databases including miRBase, UniProt, and Rfam. C-mii provides following distinguished features. First, it comes with graphical user interfaces of well-defined pipelines for both miRNA and target identifications with reliable results. Second, it provides a set of filters allowing users to reduce the number of results corresponding to the recently proposed constraints in plant miRNA and target biogenesis. Third, it extends the standard computational steps of miRNA target identification with miRNA-target folding module and GO annotation. Fourth, it supplies the bird eye views of the identification results with info-graphics and grouping information. Fifth, it provides helper functions for database update and auto-recovery to ease system usage and maintenance. Finally, it supports the multi-project and multi-thread management to improve the computational speed.

Proper citation: C-mii (RRID:SCR_010839) Copy   

•   Source: SciCrunch Registry

http://www.bnl.gov/medical/RCIBI/

Develop new scientific tools to image the movement of molecules in energy-relevant and environmentally-sensitive contexts in response to BER's call to explore the potential of radiotracer imaging in energy and environmentally-responsive contexts. Their goal is to visualize metabolic networks and regulatory systems underlying cellular communication in the living organism including plants and microbial communities. This has broad implications to DOE missions in energy and the environment and is very relevant to improvements in plant biomass for biofuel.

Proper citation: Radiotracer Chemistry Instrumentation and Biological Imaging (RRID:SCR_003258) Copy   

•   Source: SciCrunch Registry

http://www.i3crb.fr/

Project to improve data and sample exchanges and to facilitate large scale analysis of data by improving interoperability of French Biological Resources Centres (BRC or biobanks) IT systems and biological databases. The work done in this project will be linked to other national (IBiSA, ANR, R��seau des Biobanques, Club 3C-R), European (BBMRI, ELIXIR) or international project (P3G). In the preliminary phase (2009-2010) I3-CRB has developed a directory of French Biological Resource Centres / Biobanks where one may register their French BRC or perform a search across all of them. Detail by overall data or kingdom is provided as well as many filtering options. Access to biological samples is provided by the participating BRC''''s. Biological Resources Centres (BRC or biobanks) collect annotated biological samples from various sources (human, animal, plant, bacteria...). The type of samples depends on the collection and the associated thematic (DNA, proteins, cells, tissues, blood, serum, organisms...). The aims of these centers are to collect, to store, to transform and to distribute the biological samples. They constitute a vital infrastructure for life science and health research. Goals of the French Biobanks/Biological Resource Centres: * List French biobanks and their biological collections * Improve sample exchanges * Improve the international visibility of the French biological collections MeSH terms have been integrated: Domains, diseases, and location of the disease (Anatomy). Collections/species are based on NCBI Taxonomy.

Proper citation: I3-CRB: Interoperable IT Infrastructure for Biological Resources Centres / Biobanks - France (RRID:SCR_006991) Copy   

•   Source: SciCrunch Registry

http://mapman.gabipd.org/web/guest/mapman

Software tool that displays large genomics datasets (e.g. gene expression data from Arabidopsis Affymetrix arrays) onto diagrams of metabolic pathways or other biological processes.

Proper citation: MapMan (RRID:SCR_003543) Copy   

•   Source: SciCrunch Registry

http://jci-bioinfo.cn/iLoc-Plant

Data analysis service for predicting subcellular localization of plant proteins with single and multiple sites.

Proper citation: iLoc-Plant (RRID:SCR_011973) Copy   

•   Source: SciCrunch Registry

http://gpcr.biocomp.unibo.it/bacello/

A predictor for the subcellular localization of proteins in eukaryotes that is based on a decision tree of several support vector machines (SVMs). It classifies up to four localizations for Fungi and Metazoan proteins and five localizations for Plant ones. BaCelLo's predictions are balanced among different classes and all the localizations are considered as equiprobable.

Proper citation: BaCelLo (RRID:SCR_011965) Copy   

•   Source: SciCrunch Registry

http://www.csbio.sjtu.edu.cn/bioinf/Cell-PLoc/

A package of web-servers for predicting subcellular localization of proteins in different organisms.

Proper citation: Cell-PLoc (RRID:SCR_011966) Copy   

•   Source: SciCrunch Registry

http://www.gramene.org

Curated, open-source, integrated data resource for comparative functional genomics in crops and model plant species to facilitate the study of cross-species comparisons using information generated from projects supported by public funds. It currently hosts annotated whole genomes in over two dozen plant species and partial assemblies for almost a dozen wild rice species in the Ensembl browser, genetic and physical maps with genes, ESTs and QTLs locations, genetic diversity data sets, structure-function analysis of proteins, plant pathways databases (BioCyc and Plant Reactome platforms), and descriptions of phenotypic traits and mutations. The web-based displays for phenotypes include the Genes and Quantitative Trait Loci (QTL) modules. Sequence based relationships are displayed in the Genomes module using the genome browser adapted from Ensembl, in the Maps module using the comparative map viewer (CMap) from GMOD, and in the Proteins module displays. BLAST is used to search for similar sequences. Literature supporting all the above data is organized in the Literature database. In addition, Gramene now hosts a variety of web services including a Distributed Annotation Server (DAS), BLAST and a public MySQL database. Twice a year, Gramene releases a major build of the database and makes interim releases to correct errors or to make important updates to software and/or data. Additionally you can access Gramene through an FTP site.

Proper citation: Gramene (RRID:SCR_002829) Copy   

•   Source: SciCrunch Registry

http://cal.tongji.edu.cn/PlantLoc/index.jsp

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4,2023. An accurate web server for predicting plant protein subcellular localization by substantiality motif.

Proper citation: PlantLoc (RRID:SCR_003138) Copy   

•   Source: SciCrunch Registry