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http://www.biological-networks.org/pubs/suppl/sinomo/

Analysis-tool which identifies singular node motifs in a network. Network nodes can be described by node-motifs. It is an improvement to the method described in Costa et al. (2009).

Proper citation: SINOMO (RRID:SCR_005286) Copy   

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http://en.wikibooks.org/wiki/MINC/Atlases

A linear average model atlas produced by the International Consortium for Brain Mapping (ICBM) project. A set of full- brain volumetric images from a normative population specifically for the purposes of generating a model were collected by the Montreal Neurological Institute (MNI), UCLA, and University of Texas Health Science Center at San Antonio Research Imaging Center (RIC). 152 new subjects were scanned using T1, T2 and PD sequences using a specific protocol. These images were acquired at a higher resolution than the original average 305 data and exhibit improved contrast due predominately to advances in imaging technology. Each individual was linearly registered to the average 305 and a new model was formed. In total, three models were created at the MNI, the ICBM152_T1, ICBM152_T2 and ICBM152_PD from 152 normal subjects. This resulting model is now known as the ICBM152 (although the model itself has not been published). One advantage of this model is that it exhibits better contrast and better definition of the top of the brain and the bottom of the cerebellum due to the increased coverage during acquisition. The entirely automatic analysis pipeline of this data also included grey/white matter segmentation via spatial priors. The averaged results of these segmentations formed the first MNI parametric maps of grey and white matter. The maps were never made publicly available in isolation but have formed parts of other packages for some time including SPM, FSL AIR and as models of grey matter for EEG source location in VARETTA and BRAINWAVE. Again, as these models are an approximation of Talairach space, there are differences in varying areas, to continue our use of origin shift as an example, the ICBM models are approximately 152: +3.5mm in Z and +-co-ordinate -3.5mm and 2.0mm in Y as compared to the original Talairach origin. In addition to the standard analysis performed on the ICBM data, 64 of the subjects data were segmented using model based segmentation. 64 of the original 305 were manually outlined and a resulting parametric VOI atlas built. The native data from these acquisitions was 256x256 with 1mm slices. The final image resolution of this data was 181x217x181 with 1mm isotropic voxels. Refer to the ICBM152 NonLinear if you are fitting an individual to model and do not care about left/right comparisons. A short history of the various atlases that have been produced at the BIC (McConnell Brain Imaging Center, Montreal Neurological Institute) is provided.

Proper citation: MINC/Atlases (RRID:SCR_005281) Copy   

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http://www.yandell-lab.org/software/mwas.html

The MAKER Web Annotation Service (MWAS) is an easily configurable web-accessible genome annotation pipeline. It''''s purpose is to allow research groups with small to intermediate amounts of eukaryotic and prokaryotic genome sequence (i.e. BAC clones, small whole genomes, preliminary sequencing data, etc.) to independently annotate and analyze their data and produce output that can be loaded into a genome database. MWAS is build on the stand alone genome annotation pipeline MAKER, and users who wish to annotate larger datasets and whole genomes are free to download MAKER for use on their own systems. MWAS identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. MWAS can also automatically train popular gene prediction algorithms for use on new genomes for which pre-existing information is limited. MAKER is a member of the Generic Model Organism Database (GMOD) project and output produced by this site can be directly used with other GMOD tools. Annotations can be directly viewed online by the user via GBrowse, JBrowse, and Apollo, or they can be downloaded for local analysis and integration into a genome database. MWAS also supplies summary statistics on sequence features via the Sequence Ontology tool SOBA. MWAS should prove especially useful for emerging model organism genome projects with minimal bioinformatics expertise and computer resources, since a user can produce final genome annotations without having to install and configure any software locally.

Proper citation: MAKER Web Annotation Service (RRID:SCR_005318) Copy   

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http://fcon_1000.projects.nitrc.org/indi/adhd200/index.html#

A grassroots initiative dedicated to accelerating the scientific community''''s understanding of the neural basis of ADHD through the implementation of open data-sharing and discovery-based science. They believe that a community-wide effort focused on advancing functional and structural imaging examinations of the developing brain will accelerate the rate at which neuroscience can inform clinical practice. The ADHD-200 Global Competition invited participants to develop diagnostic classification tools for ADHD diagnosis based on functional and structural magnetic resonance imaging (MRI) of the brain. Applying their tools, participants provided diagnostic labels for previously unlabeled datasets. The competition assessed diagnostic accuracy of each submission and invited research papers describing novel, neuroscientific ideas related to ADHD diagnosis. Twenty-one international teams, from a mix of disciplines, including statistics, mathematics, and computer science, submitted diagnostic labels, with some trying their hand at imaging analysis and psychiatric diagnosis for the first time. The data for the competition was provided by the ADHD-200 Consortium. Consortium members from institutions around the world provided de-identified, HIPAA compliant imaging datasets from almost 800 children with and without ADHD. A phenotypic file including all of the test set subjects and their diagnostic codes can be downloaded. Winner is presented. The ADHD-200 consortium included: * Brown University, Providence, RI, USA (Brown) * The Kennedy Krieger Institute, Baltimore, MD, USA (KKI) * The Donders Institute, Nijmegen, The Netherlands (NeuroImage) * New York University Medical Center, New York, NY, USA (NYU) * Oregon Health and Science University, Portland, OR, USA (OHSU) * Peking University, Beijing, P.R.China (Peking 1-3) * The University of Pittsburgh, Pittsburgh, PA, USA (Pittsburgh) * Washington University in St. Louis, St. Louis, MO, USA (WashU)

Proper citation: ADHD-200 Sample (RRID:SCR_005358) Copy   

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https://www.psych.udel.edu/graduate/areas-of-study/behavioral-neuroscience/nature-and-goals-of-the-program

Ph.D. program in Behavioral Neuroscience is committed to training exceptional students for independent neuroscience research careers in academic, governmental, or industrial settings. Our program provides training in biological foundations of behavior, with particular focus on sensation, learning and memory, affect, development, and neural plasticity.

Proper citation: University of Delaware Behavioral Neuroscience Graduate Program (RRID:SCR_005353) Copy   

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http://users-birc.au.dk/biopv/php/fabox/

Tools for splitting, joining and otherwise manipulating FASTA format sequence files. The first tools in the toolbox is for manipulating fasta headers, cropping alignments and doing some sequence comparison allowing users to combine the description of data (often in excel spreadsheets) with the actual data (often DNA sequences). Also, producing correct input files for a range of programs seems to be problematic for the average user. Hence, some converters in some of the services have been included as well as some stand-alone converters. The converters are not necessarily meant to provide the final input file, but you''ll get a valid input file for Arlequin, MrBayes etc. - that you may further edit so it suit your needs. This means that you may need to combine several of the tools to finish your handling - but it keeps it relatively simple to use. Please note that FaBox is written in PHP and ONLY RUNS ON A WEBSERVER.

Proper citation: FaBox (RRID:SCR_005350) Copy   

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http://www.cdrewu.edu/

A private, nonprofit, nonsectarian, Historically Black College and University and a Minority Serving Institution located in Willowbrook, unincorporated Los Angeles County, California, United States.

Proper citation: Charles R. Drew University of Medicine and Science; California; USA (RRID:SCR_005346) Copy   

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http://info.gersteinlab.org/PeakSeq

A software program for identifying and ranking peak regions in ChIP-Seq experiments. It takes as input, mapped reads from a ChIP-Seq experiment, mapped reads from a control experiment and outputs a file with peak regions ranked with increasing Q-values.

Proper citation: PeakSeq (RRID:SCR_005349) Copy   

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http://arrowsmith.psych.uic.edu/cgi-bin/arrowsmith_uic/AnneOTate.cgi

A web based search tool to help you gain an overview of the set of articles (up to 25,000 most recent articles) retrieved by a PubMed query. Once you enter a query, you can select different types of summary information to view: Important words, Topics, Authors, Affiliations, Journals, Year, Clustered by topic.

Proper citation: Anne O'Tate (RRID:SCR_005340) Copy   

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http://cgs.csail.mit.edu/gem/

Java software for studying protein-DNA interaction using ChIP-seq / ChIP-exo data. It links binding event discovery and motif discovery with positional priors in the context of a generative probabilistic model of ChIP data and genome sequence, resolves ChIP data into explanatory motifs and binding events at unsurpassed spatial resolution. GEM reciprocally improves motif discovery using binding event locations, and binding event predictions using discovered motifs.

Proper citation: GEM (RRID:SCR_005339) Copy   

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http://www.csuci.edu/

Public university in Ventura County, California. CSUCI opened in 2002 as the 23rd campus in the California State University system.

Proper citation: California State University Channel Islands; California; USA (RRID:SCR_011129) Copy   

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https://dnacenter.com/blog/ddc-medical-ddc-one-worlds-largest-dna-testing-companies-supports-prostate-cancer-foundation-pcf-cell-line-authentication-initiative/

DDC Medical, division of DNA Diagnostics Center (DDC), provides STR DNA testing, supports Prostate Cancer Foundation (PCF) Cell Line Authentication Initiative (CLAI), by offering free Human Cell Line Authentication and Mycoplasma Detection testing to the PCF’s grant recipients. Provides private DNA paternity and other DNA tests for human and animal testing services accessible to clients all over the world.

Proper citation: DDC Medical (RRID:SCR_011009) Copy   

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http://www.anl.gov/

For six decades, the U.S. Department of Energy''s (DOE''s) Argonne National Laboratory has excelled in conducting scientific research in support of a secure future for the nation. From Argonne''s inception, the University of Chicago has managed and operated the laboratorya laboratory that has become a scientific leader for DOE and the country. Achievements and honors earned by Argonne researchers include three Nobel Prizes, 90 R&D 100 awards, 700 national and international awards and honors, 750 patents and the start of over 30 small businesses. Argonne National Laboratory, one of the U.S. Department of Energy''s oldest and largest national laboratories for science and engineering research, employs roughly 3,200 employees, including about 1,000 scientists and engineers, three-quarters of whom hold doctoral degrees. Argonne''s mission is to apply a unique mix of world-class science, engineering and user facilities to deliver innovative research and technologies. We create new knowledge that addresses the most important scientific and societal needs of our nation. Research at Argonne centers around three principal areas: *Energy ** Energy Storage: Argonne develops transformational energy storage systems that enable and enhance electric-drive vehicles and a green-energy grid through electrical energy storage development, prototype and manufacturing process engineering, stationary storage and grid management, and electric transportation systems. ** Alternative Energy and Efficiency: Argonne is developing the next generation of alternative energy sources to promote energy independence through improved chemical fuels, advanced biofuels, and solar energy systems, as well as through the optimization of fuel and engine dynamics. ** Nuclear Energy: Argonne develops advanced reactor and fuel cycle systems including fast reactor and fuel cycle technologies, advanced modeling and simulation methods, and innovative nuclear energy systems to enable the safe and sustainable generation of nuclear energy. * Biological and Environmental Systems: Argonne produces integrated molecular-scale, hydrological, economic and social computational models to enable regionally focused ecological and climate assessments through metagenome analysis, protein discovery, regional climate prediction and integrated climate, energy and economic discovery. * National Security: Argonne provides critical security technologies that prevent and mitigate events with potential for mass disruption or destruction through the nonproliferation and forensics of weapons of mass destruction, decision sciences, new sensors and materials, and cyber security.

Proper citation: Argonne National Laboratory (RRID:SCR_011095) Copy   

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http://www.arc.org.uk/

http://www.arc.org.uk/

Proper citation: Arthritis research campaign (RRID:SCR_011097) Copy   

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http://www.aston.ac.uk/

Public research university situated in the city centre of Birmingham, England. Aston began as the Birmingham Municipal Technical School in 1895, evolving into the UK's first College of Advanced Technology in 1956

Proper citation: Aston University; Birmingham; United Kingdom (RRID:SCR_011098) Copy   

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http://www.vet.cornell.edu/

Cornell University''s College of Veterinary Medicine''s strength as a leader in veterinary medical education, animal medicine, biomedical research and public health springs from the aggregate strengths of its departments and programs; the achievements of its faculty, alumni, and students; and its commitment to diversity and inclusiveness. At the Cornell College of Veterinary Medicine, basic scientific research meets the clinical and research demands of human and animal health. Consistently ranked among the top veterinary colleges in the country, the College is also a leader in biomedical research. The Biological & Biomedical Sciences Graduate Program fosters an atmosphere of collaboration, focusing on the interface between scientific research and clinical practice as well as a commitment to animal and human health. Graduate students contribute to this pursuit through their PhD research projects and continue to impact the world in their post graduate careers in academia, government and business.

Proper citation: Cornell University College of Veterinary Medicine (RRID:SCR_011131) Copy   

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http://www.calacademy.org/

The California Academy of Sciences is a multifaceted scientific institution committed to leading-edge research, to educational outreach, and to finding new and innovative ways to engage and inspire the public. This world-class scientific and cultural institution is based in San Francisco and recently opened a new facility in Golden Gate Park that houses an aquarium, a planetarium a natural history museum and a 4-story rainforest all under one roof. The new facility is also home to the Academy''s staff of world-class scientists, an education department that provides a wide range of student and teacher services, and an extensive science library with over 26 million specimens and artifacts. The Academy is an international center for scientific education and research and is at the forefront of efforts to understand and protect the diversity of Earth''s living things. The Academy has a staff of over 50 professional educators and Ph.D.-level scientists, supported by more than 100 Research and Field Associates and over 300 Fellows. It hosts 11 fields of research, including anthropology, aquatic biology, botany, comparative genomics, entomology, geology, herpetology, ichthyology, invertebrate zoology,mammalogy and ornithology. The Academy''s research collections, which are among the world''s largest, include more than 26 million specimensessential tools for comparative studies on the history and future of the natural world.

Proper citation: California Academy of Sciences (RRID:SCR_011132) Copy   

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https://www.linkedin.com/company/labcrew-science-management

THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 3rd,2022. Company specialized in industrial applications of electromagnetic radiation produced at synchrotron facilities.

Proper citation: LabCrew Science Management (RRID:SCR_011012) Copy   

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http://www.aiims.edu/

An autonomous institution established through an Act of Parliament to serve as a nucleus for nurturing excellence in all aspects of health care. The object was to develop patterns of teaching in Undergraduate and Post-graduate Medical Education in all its branches so as to demonstrate a high standard of Medical Education in India; to bring together in one place educational facilities of the highest order for the training of personnel in all important branches of health activity; and to attain self-sufficiency in Post-graduate Medical Education. The Institute has comprehensive facilities for teaching, research and patient-care. As provided in the Act, AIIMS conducts teaching programs in medical and para-medical courses both at undergraduate and postgraduate levels and awards its own degrees. Teaching and research are conducted in 42 disciplines. In the field of medical research AIIMS is the lead, having more than 600 research publications by its faculty and researchers in a year. AIIMS also runs a College of Nursing and trains students for B.Sc.(Hons.) Nursing post-certificate) degrees. Twenty-five clinical departments including four super specialty centers manage practically all types of disease conditions with support from pre- and Para-clinical departments. However, burn cases, dog-bite cases and patients suffering from infectious diseases are not entertained in the AIIMS Hospital. AIIMS also manages a 60-bed hospital in the Comprehensive Rural Health Centre at Ballabgarh in Haryana and provides health cover to about 2.5 lakh population through the Centre for Community Medicine.

Proper citation: All India Institute of Medical Sciences; New Delhi; India (RRID:SCR_011091) Copy   

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http://www.american.edu/

Private research university in Washington, D.C. Its main campus spans 90 acres on Ward Circle, in the Spring Valley neighborhood of Northwest D.C. Affiliated with the United Methodist Church but religious affiliation is not a criterion for admission.

Proper citation: American University; Washington D.C.; USA (RRID:SCR_011092) Copy   

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