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Consortium bringing together academic and industry researchers to advance the understanding of disease causing factors and disease progression in Rheumatoid Arthritis (RA), with a focus on accelerating the development of new drugs. The efforts under this consortium aim to develop: (1) animal models; (2) human biobanks, databases and technologies; (3) research network to address critical biologic and clinical questions; (4) community to network patients and companies. The focus will be the development of new diagnostic methods to discover the early forms of RA as well as tools to separate the different forms of RA, where different molecular mechanisms are involved and where different therapies may be required. The ultimate goal for therapeutic development is to identify the disease-causing molecular events early in the disease and then influence immunity and inflammation so that functional deterioration is halted, immunity is re-regulated and the disease is cured. Samples from biobanks will be analysed in vitro and models will be aligned with different variants of human arthritis. In addition, new models will be established using similar molecular pathways as the relevant human arthritis subsets, leading to the understanding of the etiology and early pathology of the disease for a program aimed at early and curative treatment of RA and RA-like diseases. A major focus of these efforts will be to understand and subsequently alter the adaptive immune reactions in patients from a disease-inducing mode into either a protective mode against the disease or become asymptomatic.
Proper citation: Be The Cure (RRID:SCR_003746) Copy
Oligonucleotide design software that calculates optimal oligonucleotides for a range of tasks: sequence assembly, differential expression, and microarrays (cDNA and spotted oligos)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Osprey (RRID:SCR_003627) Copy
A set of Python software packages that takes large sets of overlapping images in 2D and 3D and produces registered (aligned) 3D volumes at any size and scale. These tools were originally designed to construct 3D connectomics volumes from terabytes of image data for the Marc lab at the University of Utah Moran Eye Center.
Proper citation: Nornir (RRID:SCR_003585) Copy
https://github.com/jamesra/nornir-buildmanager/wiki
Software package that constructs 2D and 3D datasets from 2D image mosaics using the nornir tools. This produces a set of images and transforms on disk which can be accessed via Viking, HTTP, or written as a stack of images.
Proper citation: nornir-buildmanager (RRID:SCR_003584) Copy
Software tool for the visualization and annotation of 3D image data and was developed for the rapid reconstruction of neural morphology and connectivity. By dynamically loading only data from the surround of the current view point, seamless navigation is not limited to datasets that fit into the available RAM but works with much larger dataset stored in a special format on disk. Currently, KNOSSOS is limited to 8-bit data. In addition to viewing and navigating, KNOSSOS allows efficient manual neurite annotation (''skeletonization''). KNOSSOS is being used mostly for reconstructing cell morphologies from 3D electron microscopic data generated by Serial Block-Face Electron Microscopy (SBEM), with an occasional application to 2-photon and confocal optical microscopy data.
Proper citation: KNOSSOS (RRID:SCR_003582) Copy
http://srna-tools.cmp.uea.ac.uk/
Software tools for the analysis of high-throughput small RNA data.
Proper citation: UEA sRNA toolkit (RRID:SCR_003620) Copy
Organization that drives the development of Ontario's economy by helping create new jobs, products, services, technologies and businesses by bridging academia and industry. The program suite covers almost all stages of business development and career advancement, covering three key areas: Industry-Academic R&D Collaboration; Commercialization; and Entrepreneurship. Other key initiatives are the IBM Smart Computing Initiative and Colleges Ontario Network for Industry Innovation (CONII). In partnership with industry, OCE co-invests to commercialize innovation originating in the province's publicly funded colleges, universities and research hospitals. They also support and invest in early-stage projects, where the probability of commercial success and potential total return on innovation are substantial. Another expanding focus for OCE is the development of the next generation of innovators through their entrepreneurship fellowships and programs for students and youth across Ontario. Their efforts are focused on sectors of the economy with the greatest potential to drive Ontario's future prosperity and global competitiveness: energy and environment (including water); advanced manufacturing; advanced health technologies; and information, communications technologies and digital media. A trusted partner of government in program delivery, they are committed to advancing a whole-of-government approach as a means of streamlining funding application processes for companies and entrepreneurs.
Proper citation: Ontario Centres of Excellence (RRID:SCR_003734) Copy
http://khavarilab.stanford.edu/resources.html
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. An intersection-based pathogen detection workflow that utilizes a user-provided custom reference genome set for identification of nonhuman sequences in deep sequencing datasets. This is a package recommended for advanced users only.
Proper citation: RINS (RRID:SCR_003652) Copy
Japanese pharmaceutical company formed from the merger of Yamanouchi Pharmaceutical Co., Ltd. and Fujisawa Pharmaceutical Co., Ltd. Astellas' franchise areas are urology, immunology (transplantation), dermatology, cardiology, and infectious disease. Priority areas for R&D are infectious diseases, diabetes, gastrointestinal diseases, oncology, and diseases of the central nervous system. The company's headquarters are in Tokyo, with research centers in Tsukuba and Osaka. Clinical development is centered in Northbrook, Illinois and Leiderdorp, Netherlands. Combined revenues of the two pre-merger companies were $7.9 billion in 2004. Worldwide the company employs about 17,000 people. (Wikipedia)
Proper citation: Astellas Pharma Inc. (RRID:SCR_003769) Copy
Portal to support researchers and practitioners searching for information related to alcohol research including links to a number of databases, journals, and Web sites focused on alcohol research and related topics. Also included is a link to the archived ETOH database, the premier Alcohol and Alcohol Problems Science Database, which contains over 130,000 records and covers the period from 1972 through 2003. Included in ETOH are abstracts and bibliographic references to journal articles, books, dissertation abstracts, conference papers and proceedings, reports and studies, and chapters in edited works. ETOH's scope reflects the multidisciplinary nature of the alcohol research field. The range of subject areas contained in ETOH includes: medicine, biochemistry, psychology, psychiatry, epidemiology, sociology, anthropology, treatment, prevention, education, accidents and safety, legislation, criminal justice, public policy, and health services research. The ETOH database is indexed with vocabulary from the Alcohol and Other Drug Thesaurus: A Guide to Concepts and Terminology in Substance Abuse and Addiction (AOD Thesaurus), Third Edition. More than 5,000 terms in the AOD Thesaurus are used as ETOH descriptors. The Databases/Resources section includes databases and resources for alcohol researchers and practitioners. It includes an introduction to the National Library of Medicine's PubMed and some sample searches on alcohol to run in the PubMed database; descriptions of and links to the various databases of the National Clearinghouse for Alcohol and Drug Information (NCADI); a selection of alcohol and other drug databases with their descriptions and links; links to peer-reviewed journals most often used by alcohol researchers; and links to a selection of Web sites pertinent to the substance abuse field.
Proper citation: Alcohol and Alcohol Problems Science Database (RRID:SCR_003768) Copy
Consortium to identify early biological indicators (biomarkers) that can be used to predict the development of cancer, as an unintended and adverse response to a new drug. The use of these biomarkers that detect early carcinogenicity will hopefully accelerate drug development and increase patient safety. The project focuses on non-genotoxic carcinogenesis (NGC) specifically looking at the role of epigenetic effects that could be caused as unintended consequences of new drugs. Using a combination of molecular analysis technologies, the consortium combines expertise in the field of biomarkers, human and rodent cancer models, imaging, molecular profiling and bioinformatics. Participants will focus on liver tumors, the organ most affected by non-genotoxic carcinogenesis, during the preclinical safety evaluations of candidate-medicines. Their findings aim to facilitate tumor identification in other organs as well, in hopes of providing insights in the mechanisms of tumor growth. The main objectives of the consortium are to: * Identify early biomarkers for predicting which compounds have a potential for later cancer development * Improve the scientific basis for assessing carcinogenic potential of non-genotoxic (NGC) drugs * Identify the molecular response to NGC exposure that underpins development of early exposure biomarkers * Improve drug safety and the efficiency of drug development by advancing the development of alternative research methods
Proper citation: MARCAR (RRID:SCR_003755) Copy
A non-profit consortium of Boston academic medical centers and universities (and growing) to accelerate the healthcare innovation cycle by fostering interdisciplinary, inter-institutional collaboration among experts in translational research, medicine, science, engineering, healthcare implementation and entrepreneurship in concert with industry, foundations and government to rapidly improve patient care. It concentrates on early stage, high-risk ideas, projects and supports them through to a commercial exit from academia. It provides innovators with resources to explore, develop and implement novel technological solutions for today's most urgent healthcare problems. CIMIT is dedicated to helping develop medical technology that will help both military and civilian patients.
Proper citation: Center for Integration of Medicine and Innovative Technology (RRID:SCR_003710) Copy
http://elementsofmorphology.nih.gov/
Data set of standardized terms used to describe human morphology including definitions of terms for the craniofacies in general, the major components of the face, and the hands and feet. This provides a uniform and internationally accepted terms to describe the human phenotype.
Proper citation: elements of morphology (RRID:SCR_003707) Copy
http://synapses.clm.utexas.edu
A portal into the 3D ultrastructure of the brain providing: Anatomy of astrocytes, axons, dendrites, hippocampus, organelles, synapses; procedures of 3D reconstruction and tissue preparation; as well as an atlas of ultrastructural neurocytology (by Josef Spacek), online aligned images, and reconstructed dendrites. Synapse Web hosts an ultrastructural atlas containing more than 500 electron micrographs (added to regularly) that identify unique ultrastructural and cellular components throughout the brain. Additionally, Synapse Web has raw images, reconstructions, and quantitative data along with tutorial instructions and numerous tools for investigating the functional structure of objects that have been serial thin sectioned for electron microscopy.
Proper citation: Synapse Web (RRID:SCR_003577) Copy
A collaboration of international pharmaceutical companies, public health experts, civil society organizations, and U.S., European, and other regulatory authorities to speed the development of new and improved drug regimens for tuberculosis (TB). Its goals include creating innovative tools, including TB data standards and databases. The Initiative is built around four operating arms: Regulatory Science Consortium, Drug Development Coalition, Research Resources Group, and Drug Susceptibility Testing Group. The focus of the consortium is to: * Develop and integrate data standards * Qualify biomarkers through the Food and Drug Administration (FDA) / European Medicines Authority (EMA) * Develop quantitative disease progression (natural history) models * Create disease response metrics, develop target product profiles and supporting assays, and * Develop new pharmacokinetic/dynamic measures of drug interactions Accomplishments include: * Engaged the FDA, which has released updated regulatory guide-lines for developing new TB drug regimens with efforts to create a more favorable environment for combination regimen development * TB Alliance launched the first-ever clinical trial of a novel combination drug regimen for TB, validating the approach to regimen development set forth by CPTR, and is moving to a phase III clinical trial named STAND. * Developed and published TB data standards in collaboration with the Clinical Data Interchange Standards Consortium (CDISC). * Expanded scope to include the CPTR Rapid Drug Susceptibility Testing (RDST) Consortium and an expanded Modeling and Simulation development program. * Pursued several regulatory pathways with the FDA for the Hollow Fiber System Model for TB (HFS-TB). * Submitted a dossier to the EMA on the HFS-TB for qualification opinion consideration. * Submitted a "briefing book" to the FDA via the pre-IND process to review CPTR's data analysis plan and data inventory for liquid culture, with emphasis on time-to-positivity, as a quantitative measure of long-term outcome. * Initiated planning to develop a database supporting the RDST Consortium's goal to develop a rapid TB drug susceptibility test.
Proper citation: Critical Path to TB Drug Regimens (RRID:SCR_003698) Copy
http://www.sinobiological.com/
An Antibody supplier
Proper citation: Sino Biological (RRID:SCR_003697) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 27th, 2023. Cubist Pharmaceuticals was American biopharmaceutical company that targeted pathogens like MRSA. Company employed 638 people, mostly in Lexington, MA. On 8 December 2014, Merck acquired Cubist.
Proper citation: Cubist Pharmaceuticals (RRID:SCR_003691) Copy
http://jexpress.bioinfo.no/site/
Gene expression analysis software using Java.
Proper citation: J-Express (RRID:SCR_003609) Copy
Agency that produces evidence to make health care safer, higher quality, more accessible, equitable, and affordable. Funding opportunities, grants, and a large collection of longitudinal hospital care data in the United States including the Systematic Review Data Repository and data sources on healthcare cost, quality, and accessibility, emergency room visits, hospitalization, and medical insurance are available. It works within the U.S. Department of Health and Human Services and with other partners to make sure that the evidence is understood and used.
Proper citation: Agency for Healthcare Research and Quality (RRID:SCR_003604) Copy
Initiative to improve the safety of drugs on the market that utilized information drawn from patient medical record databases and health insurance claims to develop and test methods to detect and evaluate drug safety issues over time. The OMOP pilot project focused on the following objectives: * Defining and evaluating analytical methods that can be used to identify associations between drugs and health-related conditions. * Developing tools for organizing access to and evaluating the usefulness of multiple observational datasets. * Study how information from analyses of observational data can be used to inform ongoing pharmacovigilence efforts. The software tools - packaged as the OMOP Web RL Platform was developed and made available to the public, https://github.com/OMOP . In addition to these data tools, this collaborative research effort discovered methods for using data to reliably identify correlations between individual medical interventions and specific health outcomes. These insights are being used to help inform the FDA Sentinel Initiative as part of the Innovation in Medical Evidence Development and Surveillance (IMEDS) program. The achievements of the program include: * Establishment of a common data model and creation of data characterization tools, and vocabulary mappings * Implementation of Health Outcome of Interest definitions, including a program to implement these definitions as part of the Regularized Identification of Cohorts (RICO) * Release of 14 analysis methods to evaluate the performance of methods and data in identifying drug safety issues
Proper citation: Observational Medical Outcomes Partnership (RRID:SCR_003724) Copy
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