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http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/

Consortium that puts sequences into a chromosome context and provides the best possible reference assembly for human, mouse, and zebrafish via FTP. Tools to facilitate the curation of genome assemblies based on the sequence overlaps of long, high quality sequences.

Proper citation: Genome Reference Consortium (RRID:SCR_006553) Copy   

•   Source: SciCrunch Registry

http://www.asm.org/

The American Society for Microbiology is the oldest and largest single life science membership organization in the world. Membership has grown from 59 scientists in 1899 to more than 39,000 members today, with more than one third located outside the United States. The members represent 26 disciplines of microbiological specialization plus a division for microbiology educators. Eligibility for Full Membership is open to any person who is interested in microbiology and holds at least a bachelor''s degree or equivalent experience in microbiology or related field. Many members hold advanced degrees, including a large number at the master''s, PhD, ScD, DrPH and MD level. A regularly matriculated student of microbiology or a related field is eligible to become a student member. There are also separate membership categories for postdoctoral fellows and for transitional scientists in the early years of a career. Microbiologists study microbes--bacteria, viruses, rickettsiae, mycoplasma, fungi, algae and protozoa--some of which cause diseases, but many of which contribute to the balance of nature or are otherwise beneficial. Microbiological research includes infectious diseases, recombinant DNA technology, alternative methods of energy production and waste recycling, new sources of food, new drug development, and the etiology of sexually transmitted diseases, among other areas. Microbiology is also concerned with environmental problems and industrial processes. Microbiology boasts some of the most illustrious names in the annals of science--Pasteur, Koch, Fleming, Leeuwenhoek, Lister, Jenner and Salk--and some of the greatest achievements for mankind. Within the 20th century, a third of all Nobel Prizes in Physiology or Medicine have been bestowed upon microbiologists. The mission of the American Society for Microbiology is to advance the microbiological sciences as a vehicle for understanding life processes and to apply and communicate this knowledge for the improvement of health and environmental and economic well being worldwide. To achieve these goals, ASM will: * Support programs of education, training and public information; * Publish journals and books; convene meetings, workshops and colloquia; * Promote the contributions and promise of the microbiological sciences; * Recognize achievement and distinction among its practitioners; * Set standards of ethical and professional behavior.

Proper citation: American Society for Microbiology (RRID:SCR_006551) Copy   

•   Source: SciCrunch Registry

http://www.geenivaramu.ee/en/tools/gwama

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software tool for meta analysis of whole genome association data.

Proper citation: GWAMA (RRID:SCR_006624) Copy   

•   Source: SciCrunch Registry

http://gmd.mpimp-golm.mpg.de/

It facilitates the search for and dissemination of mass spectra from biologically active metabolites quantified using Gas chromatography (GC) coupled to mass spectrometry (MS). Use the Search Page to search for a compound of your interest, using the name, mass, formula, InChI etc. as query input. Additionally, a Library Search service enables the search of user submitted mass spectra within the GMD. In parallel to the library search, a prediction of chemical sub-groups is performed. This approach has reached beta level and a publication is currently under review. Using several sub-group specific Decision Trees (DTs), mass spectra are classified with respect to the presence of the chemical moieties within the linked (unknown) compound. Prediction of functional groups (ms analysis) facilitates the search of metabolites within the GMD by means of user submitted GC-MS spectra consisting of retention index (n-alkanes, if vailable) and mass intensities ratios. In addition, a functional group prediction will help to characterize those metabolites without available reference mass spectra included in the GMD so far. Instead, the unknown metabolite is characterized by predicted presence or absence of functional groups. For power users this functionality presented here is exposed as soap based web services. Functional group prediction of compounds by means of GC-EI-MS spectra using Microsoft analysis service decision trees All currently available trained decision trees and sub-structure predictions provided by the GMD interface. Table describes the functional group, optional use of an RI system, record date of the trained decision tree, number of MSTs with proportion of MSTs linked to metabolites with the functional group present for each tree. Average and standard deviation of the 50-fold CV error, namely the ratio false over correctly sorted MSTs in the trained DT, are listed. The GMD website offers a range of mass spectral reference libraries to academic users which can be downloaded free of charge in various electronic formats. The libraries are constituted by base peak normalized consensus spectra of single analytes and contain masses in the range 70 to 600 amu, while the ubiquitous mass fragments typically generated from compounds carrying a trimethylsilyl-moiety, namely the fragments at m/z 73, 74, 75, 147, 148, and 149, were excluded.

Proper citation: GMD (RRID:SCR_006625) Copy   

•   Source: SciCrunch Registry

http://espript.ibcp.fr/ESPript/ESPript/

A utility, whose output is a PostScript file of aligned sequences with graphical enhancements. Its main input is an ascii file of pre-aligned sequences. Optional files allow further rendering. The program calculates a similarity score for each residue of the aligned sequences. The output shows: * Secondary Structures * Aligned sequences * Similarities * Accessibility * Hydropathy * User-supplied markers * Intermolecular contacts In addition, similarity score can be written in the bfactor column of a pdb file, to enable direct display of highly conserved areas. You can run ESPript from this server with the HTML interface. It is configured for a maximum of 1,000 sequences. Links to webESPript * ENDscript: you can upload a PDB file or enter a PDB code such as 1M85. The programs DSSP and CNS are executed via the interface, so as to obtain an ESPript figure with a lot of structural information (secondary structure elements, intermolecular contacts). You can also find homologous sequences with a BLAST search, perform multiple sequence alignments with MULTALIN or CLUSTALW and create an image with BOBSCRIPT or MOLSCRIPT to show similarities on your 3D structure. * ProDom: you can enter a sequence identifier to find homologous domains, perform multiple sequence alignments with MULTALIN and click on the link to ESPript. * Predict Protein: you can receive a mail in text (do not use the HTML option when you submit your request in Predict Protein) with aligned sequences and numerous information including secondary structure prediction. Click on a special html link to upload your mail in ESPript. * NPS(at): you can execute the programs BLAST and CLUSTALW to obtain multiple alignments. You can predict secondary structure elements and click on the link to ESPript. This program started in the laboratory of Dr Richard Wade at the Institut de Biologie Structurale, Grenoble. It moved later to the Laboratory of Molecular Biophysics in Oxford, then to the Institut de Pharmacologie et de Biologie Structurale in Toulouse. It is now developed in the Laboratoire de BioCristallographie of Dr Richard Haser, Institut de Biologie et de Chimie des Prot��������ines, Lyon and in the Laboratoire de Biologie Mol��������culaire et de Relations Plantes-Organismes, group of Dr Daniel Kahn, Institut National de la Recherche Agronomique de Toulouse.

Proper citation: ESPript 2.2 (RRID:SCR_006587) Copy   

•   Source: SciCrunch Registry

http://edamontology.org/

An ontology of bioinformatics operations (tool, application, or workflow functions), types of data including identifiers, topics (application domains), and data formats. The applications of EDAM are within organizing tools and data, finding suitable tools in catalogues, and integrating them into complex applications or workflows. Semantic annotations with EDAM are applicable to diverse entities such as for example Web services, databases, programmatic libraries, standalone tools and toolkits, interactive applications, data schemas, data sets, or publications within bioinformatics. Annotation with EDAM may also contribute to data provenance, and EDAM terms and synonyms can be used in text mining. EDAM - and in particular the EDAM Data sub-ontology - serves also as a markup vocabulary for bioinformatics data on the Semantic Web.

Proper citation: EDAM Ontology (RRID:SCR_006620) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/BDO

Ontology that provides a comprehensive and formal representation of the different domain concepts involved in documenting the full complexity of the skeletal dysplasia domain. It captures and combines the genetic features that discriminate the bone dysplasias with the multitude of phenotypic characteristics manifested by patients and required to be taken into account in order to support the diagnosis process.

Proper citation: Bone Dysplasia Ontology (RRID:SCR_006588) Copy   

•   Source: SciCrunch Registry

https://www.prospecbio.com/

An Antibody supplier

Proper citation: ProSpec (RRID:SCR_006584) Copy   

•   Source: SciCrunch Registry

http://www.jisc.ac.uk/whatwedo/programmes/mrd/clip/webtracks.aspx

This project will develop an approach and mechanism to address the construction and propagation of linked data in the context of research and academic endeavour. The proposed work will build experiments in previous projects (Claddier, StoreLink) to develop a peer-to-peer protocol to underpin the construction of a web of linked data. This set of semantically annotated links between data resources forms a graph of citation and provenance and the project will build value added services to exploit these features. The project will address the following specific objectives: * To specify and implement the Intercom Protocol so that it can communicate a range of types of semantic links between resources via a secure communication mechanism. * To develop a practical working scenario involving data repositories, publication repositories, open science notebooks and publishers. * To develop aggregation techniques supporting added value services in search and impact analysis. * To evaluate of the approach with the identified stakeholders groups.

Proper citation: Webtracks (RRID:SCR_006615) Copy   

•   Source: SciCrunch Registry

http://www.thegpm.org/

The Global Proteome Machine Organization was set up so that scientists involved in proteomics using tandem mass spectrometry could use that data to analyze proteomes. The projects supported by the GPMO have been selected to improve the quality of analysis, make the results portable and to provide a common platform for testing and validating proteomics results. The Global Proteome Machine Database was constructed to utilize the information obtained by GPM servers to aid in the difficult process of validating peptide MS/MS spectra as well as protein coverage patterns. This database has been integrated into GPM server pages, allowing users to quickly compare their experimental results with the best results that have been previously observed by other scientists.

Proper citation: Global Proteome Machine Database (GPM DB) (RRID:SCR_006617) Copy   

•   Source: SciCrunch Registry

http://www.usrds.org/

Annual report, standard analysis files and an online query system from the national data registry on the end-stage renal disease (ESRD) population in the U.S., including treatments and outcomes. The Annual Data Report is divided into two parts. The Atlas section displays data using graphs and charts. Specific chapters address trends in ESRD patient populations, quality of ESRD care, kidney transplantation outcomes, costs of ESRD care, Healthy People 2010 objectives, chronic kidney disease, pediatric ESRD, and cardiovascular disease special studies. The Reference Tables are devoted entirely to the ESRD population. The RenDER (Renal Data Extraction and Referencing) online data query system allows users to build data tables and maps for the ESRD population. National, state, and county level data are available. USRDS staff collaborates with members of Centers for Medicare & Medicaid Services (CMS), the United Network for Organ Sharing (UNOS), and the ESRD networks, sharing datasets and actively working to improve the accuracy of ESRD patient information.

Proper citation: United States Renal Data System (RRID:SCR_006699) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/release/bioc/html/casper.html

Software to infer alternative splicing from paired-end RNA-seq data. The model is based on counting paths across exons, rather than pairwise exon connections, and estimates the fragment size and start distributions non-parametrically, which improves estimation precision.

Proper citation: casper (RRID:SCR_006613) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/miriam/

A set of online services created in support of MIRIAM, a set of guidelines for the annotation and curation of computational models. The core of MIRIAM Resources is a catalogue of data types (namespaces corresponding to controlled vocabularies or databases), their URIs and the corresponding physical URLs or resources. Access to this data is made available via exports (XML) and Web Services (SOAP). MIRIAM Resources are developed and maintained under the BioModels.net initiative, and are free for use by all. MIRIAM Resources are composed of four components: a database, some Web Services, a Java library and this web application. * Database: The core of the system is a MySQL database. It allows us to store the data types (which can be controlled vocabularies or databases), their URIs and the corresponding physical URLs, and other details such as documentation and resource identifier patterns. Each entry contains a diverse set of details about the data type: official name and synonyms, root URI, pattern of identifiers, documentation, etc. Moreover, each data type can be associated with several resources (or physical locations). * Web Services: Programmatic access to the data is available via Web Services (based on Apache Axis and SOAP messages). In addition, REST-based services are currently being developed. This API allows one to not only resolve model annotations, but also to generate appropriate URIs, based upon the provision of a resource name and accession number. A list of available web services, and a WSDL are provided. A browser-based online demonstration of the Web Services is also available to try. * Java Library: A Java library is provided to access the Web Services. The documentation explains where to download it, its dependencies, and how to use it. * Web Application: A Web application, using an Apache Tomcat server, offers access to the whole data set via a Web browser. It is possible to browse by data type names as well as browse by tags. A search engine is also provided.

Proper citation: MIRIAM Resources (RRID:SCR_006697) Copy   

•   Source: SciCrunch Registry

https://www.nimhgenetics.org/

Collaborative venture between the National Institute of Mental Health (NIMH) and several academic institutions. Repository facilitates psychiatric genetic research by providing patient and control samples and phenotypic data for wide-range of mental disorders and Stem Cells.Stores biosamples, genetic, pedigree and clinical data collected in designated NIMH-funded human subject studies. RGR database likewise links to other repositories holding data from same subjects, including dbGAP, GEO and NDAR. Allows to access these data and biospecimens (e.g., lymphoblastoid cell lines, induced pluripotent cell lines, fibroblasts) and further expand genetic and molecular characterization of patient populations with severe mental illness.

Proper citation: NIMH Repository and Genomics Resources (RRID:SCR_006698) Copy   

•   Source: SciCrunch Registry

http://bactibase.pfba-lab-tun.org/main.php

Data repository of bacteriocin natural antimicrobial peptides and includes data collected from published literature as well as high-throughput datasets. The database provides a manually curated annotation of bacteriocin sequences. New bacteriocin submissions are welcome. Various tools have been incorporated for bacteriocin analysis, such as homology search, multiple sequence alignments, Hidden Markov Models, molecular modelling and retrieval through our taxonomy Browser. BACTIBASE should be a useful tool in food preservation or food safety applications and could have implications for the development of new drugs for medical use. BACTIBASE contains calculated or predicted physicochemical properties of 218 bacteriocins produced by both Gram-positive (194) and Gram-negative bacteria (19). They also note the presence of three bacteriocins from the Archaea domain. The database now comprises 31 genera (2009).

Proper citation: BACTIBASE (RRID:SCR_006694) Copy   

•   Source: SciCrunch Registry

http://www.prosci-inc.com/

An Antibody supplier

Proper citation: ProSci (RRID:SCR_006609) Copy   

•   Source: SciCrunch Registry

https://www.iedb.org/

Repository contains antibody/B cell and T cell epitope information and epitope prediction and analysis tools. Immune epitopes are defined as molecular structures recognized by specific antigen receptors of the immune system, namely antibodies, B cell receptors, and T cell receptors. Immune epitopes from infectious diseases, excluding HIV, and immune-mediated diseases and the accompanying biological information are included.

Proper citation: Immune Epitope Database and Analysis Resource (IEDB) (RRID:SCR_006604) Copy   

•   Source: SciCrunch Registry

http://www.blueprint.org/

This website is a life-sciences research wiki hosted on Google Sites and managed by Principal Investigator Christopher Hogue at the National University of Singapore''''s Department of Biological Sciences on behalf of the Mechanobiology Institute of Singapore. Mechanobiology is the study of cellular and molecular systems that either respond to or generate forces. One of the major efforts of the Mechanobiology Institute is THE MANUAL OF CELLULAR AND MOLECULAR FUNCTION, a Wiki inspired online text resource. Brief History: Between 1997-2007 the Hogue Laboratory was located at Mount Sinai Hospital in Toronto where we developed BIND and other bioinformatics resources. Dr. Hogue was affiliated with the University of Toronto as a non-tenure track Associate Professor. Facing funding and staffing cutbacks in 2005, the intellectual property amassed by the group was sold by Mount Sinai Hospital & founders to Thomson-Reuters Scientific in March of 2007. In late 2007 Dr. Hogue moved to Singapore where he is now tenure-track faculty in Southeast Asia''''s Premiere Research University - the National Unviversity of Singapore.

Proper citation: Christopher Hogues Research Lab at the National University of Singapore (RRID:SCR_006725) Copy   

•   Source: SciCrunch Registry

https://www.progen.com/

Antibody and density gradient media supplier.

Proper citation: Progen (RRID:SCR_006726) Copy   

•   Source: SciCrunch Registry

http://www.casacolumbia.org

A science-based organization focused on developing effective solutions to address the disease of addiction and reduce the risks associated with substance use. CASAColumbia works to: * Close the gap between what is known about addiction and what is actually done to prevent and treat it * Incorporate addiction prevention and treatment into routine health care and medical practice * Explore the possibility of finding a cure Founded by Former U.S. Secretary of Health, Education, and Welfare Joseph A. Califano, Jr., CASA remains the only national organization that assembles under one roof all of the professional skills needed to research and develop proven, effective ways to prevent and treat substance abuse and addiction to all substances - alcohol, nicotine as well as illegal, prescription and performance enhancing drugs - in all sectors of society. CASAColumbia is committed to understanding the science of addiction and its implications for health care, public policy and public education.

Proper citation: CASA (RRID:SCR_006607) Copy   

•   Source: SciCrunch Registry