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

Database providing a systematic and comprehensive view of morphological phenotypes regulated by plant hormones, as well as regulatory genes participating in numerous plant hormone responses. By integrating the data from mutant studies, transgenic analysis and gene ontology annotation, genes related to the stimulus of eight plant hormones were identified, including abscisic acid, auxin, brassinosteroid, cytokinin, ethylene, gibberellin, jasmonic acid and salicylic acid. Another pronounced characteristics of this database is that a phenotype ontology was developed to precisely describe all kinds of morphological processes regulated by plant hormones with standardized vocabularies. To increase the coverage of phytohormone related genes, the database has been updated from AHD to AHD2.0 adding and integrating several pronounced features: (1) added 291 newly published Arabidopsis hormone related genes as well as corrected information (e.g. the arguable ABA receptors) based on the recent 2-year literature; (2) integrated orthologues of sequenced plants in OrthoMCLDB into each gene in the database; (3) integrated predicted miRNA splicing site in each gene in the database; (4) provided genetic relationship of these phytohormone related genes mining from literature, which represents the first effort to construct a relatively comprehensive and complex network of hormone related genes as shown in the home page of our database; (5) In convenience to in-time bioinformatics analysis, they also provided links to a powerful online analysis platform Weblab that they have recently developed, which will allow users to readily perform various sequence analysis with these phytohormone related genes retrieved from AHD2.0; (6) provided links to other protein databases as well as more expression profiling information that would facilitate users for a more systematic analysis related to phytohormone research. Please help to improve the database with your contributions.

Proper citation: Arabidopsis Hormone Database (RRID:SCR_001792) Copy   

•   Source: SciCrunch Registry

https://github.com/hms-dbmi/spp

R analysis and processing package for Illumina platform Chip-Seq data.

Proper citation: SPP (RRID:SCR_001790) Copy   

•   Source: SciCrunch Registry

http://www.myexperiment.org/

Community repository and virtual research environment where scientists can safely publish their workflows and experiment plans, share them with groups and find and use those of others. Workflows, other digital objects and collections (called Packs) can be swapped, sorted and searched. It supports Linked data, has a SPARQL Endpoint and REST API and is based on an open source Ruby on Rails codebase. Scientific workflows in various formats can be uploaded. Specific support is provided for Taverna workflows for which the system displays relevant metadata, components and visual previews, that are retrieved directly from workflow files. Version history for workflows is collected. This feature allows the contributor to keep previous versions of the workflow available, when the latest one is uploaded. This brings additional benefit for the users by allowing them to view the development stages of the workflow towards its latest implementation.

Proper citation: myExperiment (RRID:SCR_001795) Copy   

•   Source: SciCrunch Registry

https://openprovenance.org/opm/

A model of provenance that is designed to meet the following requirements: (1) To allow provenance information to be exchanged between systems, by means of a compatibility layer based on a shared provenance model. (2) To allow developers to build and share tools that operate on such a provenance model. (3) To define provenance in a precise, technology-agnostic manner. (4) To support a digital representation of provenance for any "thing", whether produced by computer systems or not. (5) To allow multiple levels of description to coexist. (6) To define a core set of rules that identify the valid inferences that can be made on provenance representation.

Proper citation: Open Provenance Model (RRID:SCR_001829) Copy   

•   Source: SciCrunch Registry

http://www.pdc.kth.se/

PDC operates leading-edge, high-performance computers on a national level. PDC offers easily accessible computational resources that primarily cater to the needs of Swedish academic research and education. PDC also takes part in major international projects to develop high-performance computing for the future and stay a leading national resource in parallel computing.

Proper citation: Royal Institute of Technology: PDC (RRID:SCR_001828) Copy   

•   Source: SciCrunch Registry

https://github.com/JialiUMassWengLab/TEMP

Software package for detecting transposable elements (TEs) insertions and excisions from pooled high-throughput sequencing data.

Proper citation: TEMP (RRID:SCR_001788) Copy   

•   Source: SciCrunch Registry

https://github.com/uci-cbcl/EXTREME

A motif discovery algorithm designed to find DNA-binding motifs in ChIP-Seq and DNase-Seq data.

Proper citation: EXTREME (RRID:SCR_001821) Copy   

•   Source: SciCrunch Registry

http://www.mimg.ucla.edu/faculty/xing/glimmps/

Software to characterize the genetic variation of alternative splicing using a robust statistical method for detecting splicing quantitative trait loci (sQTLs) from RNA-seq data. It takes into account the individual variation in sequencing coverage and the noise prevalent in RNA-seq data.

Proper citation: GLiMMPS (RRID:SCR_001787) Copy   

•   Source: SciCrunch Registry

http://consc.net/online

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. This is a directory of 5311 free online papers on consciousness in philosophy and in science, and of related topics in the philosophy of mind. The papers in this directory are drawn from PhilPapers, a database of both online and offline works in philosophy. Sponsors: Sponsored by the Joint Information Systems Committee as part of the Information Environment Programme.

Proper citation: Online Papers on Consciousness (RRID:SCR_001826) Copy   

•   Source: SciCrunch Registry

http://www.wikicancer.org/

A place where people connected to cancer can share real-life experiences -- fears, insights, stories, and advice. Adding perspectives is easy, and every contribution builds the site into a more valuable and unique community resource. Content, resources, and support on wikiCancer: * Just been diagnosed with cancer? * Living with cancer * For cancer survivors * How to support someone with cancer * Connect with other cancer patients, survivors, family and caregivers

Proper citation: wikiCancer (RRID:SCR_001824) Copy   

•   Source: SciCrunch Registry

https://github.com/shka/R-SAMstrt

Software package that provides the significance analysis of sequencing data with spike-in normalization. The statistical backgrounds and the benefits depend on SAMseq of the samr package.

Proper citation: SAMstrt (RRID:SCR_001780) Copy   

•   Source: SciCrunch Registry

http://www.mindandlife.org/support/mlrn/

A project of the Mind and Life Institute, fosters multidisciplinary communication about scientific research on meditation and other contemplative practices. It is dedicated to fostering dialog and research at the highest possible level between modern science and the great living contemplative traditions, especially Buddhism. It builds on a deep commitment to the power and value of both of these ways of advancing knowledge and their potential to alleviate suffering. Membership is free, and this loose affiliation of scientists, meditators, and people interested in research promotes opportunities for researchers and meditators to communicate together. All perspectives, scientific fields, and styles of meditation are welcome. The MLRN includes cognitive neuroscientists who skillfully use scientific methods in the study of meditation, meditation scholars interested in scientific interfaces, and people who can help support meditation research. MLRN members are likely to be recruited to serve as advisors, referees, participants, and collaborators in upcoming studies on meditation. The MLRN encompasses a variety of meditation practices, and incorporates both contemplative and scientific approaches. The MLRN includes a low-volume, moderated electronic announcement list. This list maintains a high signal-to-noise ratio by distributing infrequent but important messages to large numbers of recipients. Members of this announcement list receive bibliographic updates on recent publications, announcements of upcoming conferences, calls for papers for special-issue journals and conference symposia, synopses of recent meetings, announcements of relevant email lists, websites, and other resources, and other announcements appropriate for widespread distribution. Sponsors: The Hershey Family Foundation has been patron since 1990. This Institute has received generous financial support from the Fetzer Institute, The Nathan Cummings Foundation, Branco Weiss, Adam Engle, Michael Sautman, Mr. and Mrs. R. Thomas Northcote, Christine Austin, Dennis Perlman, Marilyn and the late Don Gevirtz, Michele Grennon, Klaus Hebben, Joe and Mary Ellyn Sensenbrenner, and Edwin and Adrienne Joseph.

Proper citation: MLRN (RRID:SCR_001899) Copy   

•   Source: SciCrunch Registry

http://www.megabionet.org/atpid/webfile/

Centralized platform to depict and integrate the information pertaining to protein-protein interaction networks, domain architecture, ortholog information and GO annotation in the Arabidopsis thaliana proteome. The Protein-protein interaction pairs are predicted by integrating several methods with the Naive Baysian Classifier. All other related information curated is manually extracted from published literature and other resources from some expert biologists. You are welcomed to upload your PPI or subcellular localization information or report data errors. Arabidopsis proteins is annotated with information (e.g. functional annotation, subcellular localization, tissue-specific expression, phosphorylation information, SNP phenotype and mutant phenotype, etc.) and interaction qualifications (e.g. transcriptional regulation, complex assembly, functional collaboration, etc.) via further literature text mining and integration of other resources. Meanwhile, the related information is vividly displayed to users through a comprehensive and newly developed display and analytical tools. The system allows the construction of tissue-specific interaction networks with display of canonical pathways.

Proper citation: Arabidopsis thaliana Protein Interactome Database (RRID:SCR_001896) Copy   

•   Source: SciCrunch Registry

http://norccentral.org

Portal to research centers and core facilities specifically support obesity research and better understand the relationship between health and nutrition.

Proper citation: Nutrition and Obesity Research Centers (RRID:SCR_004131) Copy   

•   Source: SciCrunch Registry

https://www.cgl.ucsf.edu/chimera/

Software tool for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated. Chimera includes complete documentation and several tutorials.

Proper citation: UCSF Chimera (RRID:SCR_004097) Copy   

•   Source: SciCrunch Registry

http://www.eurorec.org/

An independent not-for-profit organization promoting in Europe the use of high quality Electronic Health Record systems (EHRs). One of its main missions is to support, as the European authorized certification body, EHRs certification development, testing and assessment by defining functional and other criteria. EuroRec is organized as a permanent network of National ProRec centers and provides services to industry (developers and vendors), healthcare providers (buyers), policy makers and patients.

Proper citation: EuroRec (RRID:SCR_004090) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/pmc/

Collection of full text archive of biomedical and life sciences journal literature at U.S. National Institutes of Health National Library of Medicine (NIH/NLM). With PubMed Central, NCBI is taking lead in preserving and maintaining open access to electronic literature. Value of PubMed Central, in addition to its role as an archive, lies in what can be done when data from diverse sources is stored in common format in single repository. All articles in PMC are free (sometimes on a delayed basis). Some journals go beyond free, to Open Access.

Proper citation: PubMed Central (RRID:SCR_004166) Copy   

•   Source: SciCrunch Registry

http://www.genome.jp/

GenomeNet is a Japanese network of database and computational services for genome research and related research areas in biomedical sciences, operated by the Kyoto University Bioinformatics Center. GenomeNet was established in September 1991 under the Human Genome Program of the then Ministry of Education, Science and Culture (Monbusho). The GenomeNet service has been developed by the Kanehisa Laboratory in Kyoto University as part of the research projects. GenomeNet is operated using the Supercomputer System of the Institute for Chemical Research, Kyoto University. LinkDB is supported by the National Bioscience Database Center of the Japan Science and Technology Agency.

Proper citation: GenomeNet (RRID:SCR_004165) Copy   

•   Source: SciCrunch Registry

http://epigraph.mpi-inf.mpg.de/WebGRAPH/

A software for genome and epigenome analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: EpiGRAPH (RRID:SCR_004326) Copy   

•   Source: SciCrunch Registry

http://pubchem.ncbi.nlm.nih.gov/

Collection of information about chemical structures and biological properties of small molecules and siRNA reagents hosted by the National Center for Biotechnology Information (NCBI).

Proper citation: PubChem (RRID:SCR_004284) Copy   

•   Source: SciCrunch Registry