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A collection of images of the human nervous system focusing on disease and injury.
Proper citation: Human Nervous System Disease and Injury (RRID:SCR_006370) Copy
http://www.genomesunzipped.org/
A group blog providing expert, independent commentary on the personal genomics industry. The goal of the project is to provide genetic testing consumers with independent and informed analysis of developments in the field of genetics and the genetic testing industry. Members of Genomes Unzipped include active researchers in various fields of genetics, as well as specialists in the legal and public health issues surrounding new genomic technologies. Many of us have also been extensively involved in public communication about genetics. Members of the group have had their DNA tested with a variety of products. We have released all of these genetic data openly to the public, both as raw data and in a custom genome browser. As the project proceeds we plan to obtain more genetic tests ����?? up to and including whole genome sequencing ����?? and to continue to release these data to the world. The group is also performing analyses of our own raw genetic data to illustrate fundamental concepts in genetics, using software written both by group members and other collaborators; and we����??ll be releasing the code for that software in our new code repository. As the project expands, we����??ll be looking to add data from other volunteers to the project, as well as to collaborate with other ����??genome hackers����?? on the development of new tools for exploring genetic data.
Proper citation: Genomes Unzipped (RRID:SCR_006870) Copy
Society leading the fight against kidney disease by educating health professionals, sharing new knowledge, advancing research, and advocating the highest quality care for patients. To accomplish its mission, ASN will: # Educate health professionals by increasing the value of ASN education. # Share new knowledge by improving the quality and expanding the reach of ASN''s communications, including maintaining the premier publications in kidney disease. # Promote the highest quality care by serving as the professional organization informing health policy in kidney disease. # Advance patient care and research in kidney disease by strengthening the pipeline of clinicians, researchers, and educators. To accomplish this goal, ASN will: ## Implement a strategy to increase interest in nephrology careers, which includes promoting diversity within the nephrology workforce. ## Help fund travel to ASN educational activities for physicians and researchers training in the field of kidney disease. ## Use the ASN Grants Program to support outstanding research and foster career development. # Continue to bolster the ASN infrastructure, which includes: ## Increasing diversityincluding age and experience, ethnicity, and genderat all levels of the society. ## Providing avenues for helping ASN members facilitate professional exchange. ## Expanding ASN membership. ## Increasing the ASN Council-Designated Endowment Fund (independent of operational budget) to support grants and other priorities
Proper citation: ASN - American Society of Nephrology (RRID:SCR_006709) Copy
http://www.openarchives.org/ore/
Initiative which defines standards for the description and exchange of aggregations of Web resources. The intent of the effort is to develop standards that generalize across all web-based information including the increasing popular social networks of web 2.0. The goal of these standards is to expose the rich content in these aggregations (sometimes called compound digital objects, they may combine distributed resources with multiple media types including text, images, data, and video) to applications that support authoring, deposit, exchange, visualization, reuse, and preservation. The specific aim of the ORE effort is to promote (through creation or endorsement) effective and consistent mechanisms which: facilitate discovery of compound digital objects; reference (or link to) these objects (as well as parts thereof); obtain a variety of disseminations of these objects; aggregate and disaggregate objects; and enable processing of objects by automated agents.
Proper citation: Open Archives Initiative - Object Reuse and Exchange Initiative (RRID:SCR_006982) Copy
http://titan.biotec.uiuc.edu/ESTIMA/
A web application called Expressed Sequence Tag Information Management and Annotation (ESTIMA) has been created to meet the EST annotation and data management requirements of multiple high-throughput EST sequencing projects. It is anchored on individual ESTs and organized around different properties of ESTs including chromatograms, base-calling quality scores, structure of assembled transcripts, and multiple sources of comparison to infer functional annotation, Gene Ontology associations, and cDNA library information. ESTIMA consists of a relational database schema and a set of interactive query interfaces. These are integrated with a suite of web-based tools that allow a user to query and retrieve information. Further, query results are interconnected among the various EST properties. ESTIMA has several unique features. Users may run their own EST processing pipeline, search against arbitrary reference genomes, and use any clustering and assembly algorithm. The ESTIMA database schema is very flexible and accepts output from any EST processing and assembly pipeline. ESTIMA has been used for management of EST projects of many species, including honeybee (Apis mellifera), cattle (Bos taurus), songbird (Taeniopygia guttata), corn rootworm (Diabrotica vergifera), catfish (Ictalurus punctatus, Ictalurus furcatus), and apple (Malus x domestica). The entire resource may be downloaded and used as is, or readily adapted to fit the unique needs of other cDNA sequencing projects. The scripts used to create the ESTIMA interface are freely available to academic users in an archived format from http://titan.biotec.uiuc.edu/ESTIMA/download/. The entity-relationship (E-R) diagrams and the programs used to generate the Oracle database tables are also available. Presently the chromatograms, EST databases and their annotations have been made available for cattle and honeybee.
Proper citation: ESTIMA - Expressed Sequence Tag Information Management and Annotation (RRID:SCR_007216) Copy
http://www.neuroconstruct.org/
Software for simulating complex networks of biologically realistic neurons, i.e. models incorporating dendritic morphologies and realistic cell membrane conductance, implemented in Java and generates script files for the NEURON and GENESIS simulators, with support for other simulation platforms (including PSICS and PyNN) in development. neuroConstruct is being developed in the Silver Lab in the Department of Neuroscience, Physiology and Pharmacology at UCL and uses the latest NeuroML specifications, including MorphML, ChannelML and NetworkML. Some of the key features of neuroConstruct are: Creation of networks of biologically realistic neurons, positioned in 3D space. Complex connectivity patterns between cell groups can be specified for the networks. Can import morphology files in GENESIS, NEURON, Neurolucida, SWC and MorphML format for inclusion in network models. Simulations can be run on the NEURON or GENESIS platforms. Cellular processes (synapses/channel mechanisms) can be imported from native script files or created in ChannelML. Recording of simulation data generated by the simulation and visualization/analysis of data. Stored simulation runs can be viewed and managed through the Simulation Browser interface.
Proper citation: neuroConstruct (RRID:SCR_007197) Copy
https://github.com/jstjohn/SimSeq
An illumina paired-end and mate-pair short read simulator. This project attempts to model as many of the quirks that exist in Illumina data as possible. Some of these quirks include the potential for chimeric reads, and non-biotinylated fragment pull down in mate-pair libraries .
Proper citation: SimSeq (RRID:SCR_006947) Copy
http://www.ikaros-project.org/
Ikaros is an open infrastructure for system level modeling of the brain including databases of experimental data, computational models and functional brain data. The system makes heavy use of the emerging standards for Internet based information and makes all information accessible through an open web-based interface. In addition, Ikaros can be used as a control architecture for robots which in the extension will lead to the development of a brain inspired robot architecture. The main components of the Ikaros systems are: a platform independent simulation kernel; a set of computational brain models; a set of I/O modules for interfacing with data files and peripheral such as robots or video cameras; tools for building systems of interconnected models; a plug-in architecture that allows new models to be easily added to the system; and a database with data from learning experiments that can be used for validation of the computational models.
Proper citation: Ikaros Project (RRID:SCR_007391) Copy
http://www.mcell.cnl.salk.edu/
Software modeling tool for realistic simulation of cellular signaling in complex 3-D subcellular microenvironment in and around living cells. Program that uses spatially realistic 3D cellular models and specialized Monte Carlo algorithms to simulate movements and reactions of molecules within and between cells.
Proper citation: MCell (RRID:SCR_007307) Copy
Software platform, general technologies and theoretical supports for computational biology with the grand aim to make precise whole cell simulation at the molecular level possible.Technologies include formalisms and techniques, including technologies to predict, obtain or estimate parameters such as reaction rates and concentrations of molecules in the cell. The E-Cell System is a software platform for modeling, simulation and analysis of complex, heterogeneous and multi-scale system like the cell. The E-Cell Project is open to anyone who shares the view with u that development of cell simulation technology, and, even if such ultimate goal might not be within ten years of reach yet, solving various conceptual, computational and experimental problems that will continue to arise in the course of pursuing it, may have a multitude of eminent scientific, medical and engineering impacts on our society.
Proper citation: Electronic Cell Project (RRID:SCR_007381) Copy
http://mipgsun.mipg.upenn.edu/~Vnews/
Data-, machine-, and application- independent software system for the visualization and analysis of multidimensional images. This transportable, very inexpensive software system, has capabilities for visualizing, manipulating, and analyzing multidimensional, multimodality image information. It is designed to run on Unix machines under X-windows. It uses a data protocol that is a multidimensional generalization of the ACR-NEMA standards. We have tested it extensively on SGI and Sun workstations and PCs. Other recipients of 3DVIEWNIX have installed it on a variety of platforms including IBM RS6000s, HP700s, and Stardent, all from a single source code version. UNIQUE FEATURES OF 3DVIEWNIX * Transportable - based on UNIX, X-window, and C * Based on multidimensional generalization of ACR-NEMA standards of data representation * Application-independent * Image dimensionality independent * Can handle rigid, non-rigid, static, and dynamic objects and object assemblies * Can handle object information from multiple modalities and longitudinal acquisitions * Multitudes of visualization, manipulation, and analysis methods incorporated * Open software system distributed with source code
Proper citation: 3DViewnix (RRID:SCR_007351) Copy
http://www.scienceexchange.com/facilities/microtech-lab
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 22, 2023. Microtech Lab is a laboratory open to all researchers involved in the development of genomics projects of basic, translational, and clinical research. Our lab provides the support and tools for microarray experiments for the following applications: 1) Analysis of gene expression profiles 2) Analysis of the expression profiles of microRNA (miRNA)
Proper citation: Microtech Lab (RRID:SCR_012371) Copy
International collaboration of the International Nucleotide Sequence Databases (INSD), DDBJ, ENA, and GenBank, maintained for over 18 years. Individuals submitting data to the international sequence databases should be aware of INSDC policy.
Proper citation: INSDC (RRID:SCR_011967) Copy
https://www.promab.com/about-us
Develops and commercializes recombinant proteins and custom monoclonal antibodies through integration of bioinformatics, gene cloning, protein expression and purification, and immunology, using high-throughput technologies. ProMab applies its proteins and antibodies to deliver diagnostic products as well as services targeting the global biomedical market through collaborations with other biotechnology and bio-reagent companies.
Proper citation: ProMab Biotechnologies Inc. (RRID:SCR_012380) Copy
Provides oligonucleotides. Synthesizes custom DNA/RNA oligonucleotides for scientific and therapeutic communities.
Proper citation: Oligo Factory (RRID:SCR_012567) Copy
http://www.scienceexchange.com/facilities/trevigen
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 19,2024. Trevigen Cell Assays (TCA), a division of Trevigen, Inc., was established in 2008 to conduct contract research work for the pharmaceutical, biotechnology, government and academic segments of the medical research market. TCA specializes in designing and conducting assays for lead compounds and genotoxic screening based on DNA damage and repair as well as cancer cell behavior.
Proper citation: Trevigen Cell Assays (RRID:SCR_012449) Copy
https://www.tglabs.com/home.html
TG Labs Company, located in Colorado, has two divisions Technical division and Industrial division. Technical Division operates scientific, medical and chemical discovery laboratory in Englewood, Colorado. This division also develops special devices, equipment and processes for the medical, chemical and environmental industries. We offer proven solutions from concept through full scale production, including regulatory standards.
Proper citation: TG Labs (RRID:SCR_012581) Copy
http://www.scienceexchange.com/facilities/ohio-university
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 14,2024. Portal, Core facility
Proper citation: Ohio University Labs and Facilities (RRID:SCR_012461) Copy
https://us.progen.com/About-Us/
ProGen - Protein & Gene Engineering specializes in custom molecular biology services including DNA cloning, sub-cloning, codon optimized artificial gene synthesis, site-directed mutagenesis and large scale custom projects such as DNA isolation and purification. The custom products of the company are used for gene engineering to study gene expression regulatory mechanisms, protein engineering, and analysis of gene and protein function. Customers of the company include research laboratories in academia, clinical researchers in medical institutes and biotechnology companies. In addition to our custom cloning services, as an authorized Israeli representative of SBS Genetech Co., we market molecular biology products of SBS at competitive prices. SBS is one of the largest sources of synthetic oligonucleotides. The range of the products cover biochemicals, enzymes and PCR products. As a young company we are highly motivated to deliver high quality services and products at lowest prices with a rapid schedule of delivery. We guarantee full customer satisfaction on all products and services.
Proper citation: ProGen - Protein and Gene Engineering (RRID:SCR_012405) Copy
We provide custom synthesis of peptides and peptide conjugates.
Proper citation: Ohio Peptide (RRID:SCR_012407) Copy
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