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http://www.mmc.edu/

Founded in 1876, Meharry is a non-profit university in Tennessee. Meharry includes a medical school, dental school, and a graduate school.

Proper citation: Meharry Medical College (RRID:SCR_012863) Copy   

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https://github.com/bedops/bedops

A suite of tools to address common questions raised in genomic studies - mostly with regard to overlap and proximity relationships between data sets.

Proper citation: BEDOPS (RRID:SCR_012865) Copy   

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http://www2.hu-berlin.de/eyetracking-eeg

A plugin for the open-source MATLAB toolbox EEGLAB developed with the goal to facilitate integrated analyses of electrophysiological and oculomotor data. The plugin parses, imports, and synchronizes simultaneously recorded eye tracking data and adds it as extra channels to the EEG. Saccades and fixations can be imported from the eye tracking raw data or detected with an adaptive velocity-based algorithm. Eye movements are then added as new time-locking events to EEGLAB's event structure, allowing easy saccade- and fixation-related EEG analysis (e.g., fixation-related potentials, FRPs). Alternatively, EEG data can be aligned to stimulus onsets and analyzed according to oculomotor behavior (e.g. pupil size, microsaccades) in a given trial. Saccade-related ICA components can be objectively identified based on their covariance with the electrically independent eye tracker. All functions can be accessed via EEGLAB's GUI or called from the command line.

Proper citation: EYE-EEG (combined eye-tracking & EEG) (RRID:SCR_012903) Copy   

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http://genome.dkfz-heidelberg.de/cgi-bin/GENSCAN/genscan.cgi

Resource out of service. Documented on February 24,2021.

Proper citation: GENSCAN (RRID:SCR_012902) Copy   

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http://gmod.org/wiki/Flash_GViewer

Flash GViewer is a customizable Flash movie that can be easily inserted into a web page to display each chromosome in a genome along with the locations of individual features on the chromosomes. It is intended to provide an overview of the genomic locations of a specific set of features - eg. genes and QTLs associated with a specific phenotype, etc. rather than as a way to view all features on the genome. The features can hyperlink out to a detail page to enable to GViewer to be used as a navigation tool. In addition the bands on the chromosomes can link to defineable URL and new region selection sliders can be used to select a specific chromosome region and then link out to a genome browser for higher resolution information. Genome maps for Rat, Mouse, Human and C. elegans are provided but other genome maps can be easily created. Annotation data can be provided as static text files or produced as XML via server scripts. This tool is not GO-specific, but was built for the purpose of viewing GO annotation data. Platform: Online tool

Proper citation: Flash Gviewer (RRID:SCR_012870) Copy   

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http://www.siu.edu/

Public research university in Carbondale, Illinois. Founded in 1869, SIU is the oldest campus of the Southern Illinois University system.

Proper citation: Southern Illinois University; Illinois; USA (RRID:SCR_012873) Copy   

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http://www.embl-heidelberg.de/Services/serrano/agadir/agadir-start.html

A prediction algorithm based on the helix/coil transition theory. Agadir predicts the helical behaviour of monomeric peptides. It only considers short range interactions. Conditions such as pH, temperature and ionic strength are used in the calculation. Modifications of the termini are also allowed. To submit a job to Agadir, log in the calculation part using the login button in the right bottom. Then fill-in the input form and proceed to next page, etc. You will reach a final page that resumes all the input information and allows you to run the calculation. You can submit one or more peptide sequences in one-letter format. Sequences should be separated by one return character. Spaces and tabulations are automatically removed. Only standard amino acids are accepted. Agadir accepts two modifications at the N-terminus (acetylation or succynilation), and one at the C-terminus (amidation). Just choose the desired option in the input form. You can use only one set of parameters: temperature, ionic strength (calibrated for NaCl) and pH, or explore a particular range of conditions for one parameter. In the latter case the intervals between any two values are: Ionic strength 0.05 M Temperature 1 K pH 0.2 units When setting the conditions for these parameters please be aware that the allowed ranges are: Ionic strength between 0.001 and 1 M Temperature between 273 and 400 K pH between 1 and 14 Output of the prediction at the residue level is available only when submitting no more than ten peptide sequences, and without any screening of conditions. Hstaple is the Hydrophobic Staple motif, Schellman is the Shellman motif, CaH are the expecte chemical shifts of the Calpha proton, 13Ca are the alpha Carbon 13 chemical shifts, JaN is the Jalpha--nitrogen coupling.

Proper citation: Agadir (RRID:SCR_008402) Copy   

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http://www.sp2000.org/

Species 2000 is a federation of database organizations working closely with users, taxonomists and sponsoring agencies. The goal of the Species 2000 project is to create a validated checklist of all the world''s species (plants, animals, fungi and microbes). This is being achieved by bringing together an array of global species databases covering each of the major groups of organisms. Each database covers all known species in the group, using a consistent taxonomic system. The participating databases are widely distributed throughout the world and currently number 52. The existing global species databases presently account for some 60% of the total known species, so substantial investment in new databases will be needed for full coverage of all taxa to be achieved.

Proper citation: Species 2000 (RRID:SCR_008231) Copy   

•   Source: SciCrunch Registry

http://www.vetmed.vt.edu/research/amrv.asp

An institutional training program to train veterinarians in conducting research. The program trains veterinarians in acquiring the skills of a researcher as they undergo a specific M.S. or Ph.D program. The program urges graduates to take part in research concerning animal models of infectious diseases, immunology, and nutrition, among other health topics.

Proper citation: Post-DVM Training Program on Animal Model Research for Veterinarians (RRID:SCR_008303) Copy   

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http://cran.r-project.org/web/packages/RJaCGH/index.html

Software for Bayesian analysis of CGH microarrays fitting Hidden Markov Chain models.

Proper citation: RJaCGH (RRID:SCR_008381) Copy   

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http://www.cerc.utexas.edu/OnlineCall/

A fast basecalling scheme for Illumina''s Next Generation sequencing machines, specifically designed for GAII.

Proper citation: OnlineCall (RRID:SCR_008263) Copy   

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http://www.bioinformatics.kmutt.ac.th/list-of-courses-2/

This program is an international Bioinformatics course at KMUTT designed for students who desire focused training in the elements of computer science, biology and biochemistry needed for a successful career in this exciting new discipline. Students in this program will receive comprehensive training in genomics, algorithms for sequence analysis, database design and management, software engineering and programming (including web-based development). Each student will apply their skills to a practical project, where they will design and implement a solution to a real-world problem under the guidance of an experienced mentor in industry or academia. In order to receive a Masters degree, students must demonstrate mastery of the core subject matter (expected to maintain a minimum grade of B in all core courses) and reach a minimum TOEFL test score of 500 (paper) or 173 (computer) or equivalent prior to or on completion of the course. In 24 monhs students gain the knowledge and skills necessary to enter a career with industry or a career in research as a bioinformatics or biocomputing specialist. The program offers fifteen scholarships each year include tuition and fees plus an additional to cover living expenses for 24 months. :Keywords: Bioinformatics, Computer Science, Biology, Biochemistry, Genomics, Algorithms, Sequence, Analysis, Database, Design, Management, Software, Engineering, Programing, Industry, Academia, Master''s, :

Proper citation: Bioinformatic: Programs and Courses (RRID:SCR_008379) Copy   

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http://bioinfo.cipf.es/isacghtrac

Software to analyze CNV that will now normalize arrays CGH and it will visually integrate different genome annotations.

Proper citation: IsaCGH (RRID:SCR_008375) Copy   

•   Source: SciCrunch Registry

http://www.uow.edu.au/

Public research university in New South Wales, Australia which offers degree programs across a wide spectrum of disciplines, as well as providing research facilities to scientists

Proper citation: University of Wollongong; New South Wales; Australia (RRID:SCR_008322) Copy   

•   Source: SciCrunch Registry

http://www.agingintervention.org/

A 501(c)(3) non-profit organization that gives out grants created to develop new therapies to control and reverse the causes of aging, as well as treat and prevent the diseases of aging. The goal is to eventually control the processes of aging, reverse their effects, and stay younger longer and ultimately create indefinite youthful, happy and productive lifespan using innovative scientific methods that are under development today in biotech companies and research labs around the world. The foundation also offers education on what we can do now to stay younger, live longer and be happier while new therapies are being developed.

Proper citation: Aging Intervention Foundation (RRID:SCR_008288) Copy   

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http://www.strout.net/conical/

CONICAL is a C++ class library for building simulations common in computational neuroscience. Currently its focus is on compartmental modeling, with capabilities similar to GENESIS and NEURON. Future classes may support reaction-diffusion kinetics and more. A key feature of CONICAL is its cross-platform compatibility; it has been fully co-developed and tested under Unix, DOS, and Mac OS. Any C++ compiler which adheres to the emerging ANSI standard should be able to compile the CONICAL classes without modification. It is intended to encourage the rapid development of simulator software, especially on non-Unix systems where such software is sorely lacking. The present focus of the CONICAL library of C++ classes is compartmental modeling. A model neuron is built out of compartments, usually with a cylindrical shape. When small enough, these open-ended cylinders can approximate nearly any geometry, just as the stack of cylinders approximates a cone in the logo above. While any compartment has passive electrical properties (like a simple resistor-capacitor circuit), more interesting properties require the use of active ion channels whose conductance varies as a function of the time or membrane voltage. A standard Hodgkin-Huxley ion channel is included as one of the built-in CONICAL object types. Most of the voltage-gated ion channels in the literature can be directly implemented merely by setting the parameters of this class. For extensibility, this class is derived from several layers of more general classes. Connections between neurons can be implemented in several ways. For a gap junction (i.e., simple electrical connection), a passive current (or pair of currents, one in each direction) can be used. Synapses are more complex objects, but used in a similar fashion. The Alpha-function synapse is a very popular model of synaptic transmission, and is a basic CONICAL class. More complex (and realistic) synapses can be built using the Markov-model synapse. (A Markov model can be used on its own for other purposes as well.) In addition to classes directly related to neural modeling, CONICAL contains several other useful object types. These include a current injector, and a column-oriented output stream for storing data in table form.

Proper citation: Conical: The Computational Neuroscience Class Library (RRID:SCR_008318) Copy   

•   Source: SciCrunch Registry

http://abgent.com

Antibody supplier.

Proper citation: Abgent (RRID:SCR_008393) Copy   

•   Source: SciCrunch Registry

http://www.ini.uzh.ch/

The mission of the Institute is to discover the key principles by which brains work and to implement these in artificial systems that interact intelligently with the real world. The Institute of Neuroinformatics is built of many people covering a wide range of disciplines and research areas. The major research projects and areas are listed below. - Behavior and Cognition: At the Institute of Neuroinformatics researchers investigate in Behavior and Cognition on various levels, ranging from neuronal circuit models of learning and adaptation over psychophysical experiments for color constancy up to modeling complex behavioral tasks such as exploration and goal-directed navigation. - Computation in Neural Circuits: By examining the brains of cats, rats and monkeys, and by making simulations of the cortex, INI hopes to learn how this circuit performs such widely different tasks. This knowledge might lead to advances in how computers are designed, and will certainly lead to advances in the subtlety and power of medical neuroscience. - Neurotechnologies: INI aims to harness the principles of biological computation, which can be expected to have a major impact on the technology market as autonomous intelligence pervades equipment, vehicles, buildings, utilities and clothing. Sponsors: INI is supported by European Union (EU), Gerbert Ruf Stiftung, Neuroscience Center (ZNZ), Swiss Confederation (KTI), Swiss Federal Institute of Technology Zurich (ETH), Swiss National Science Foundation (SNF), University of Zurich (UZH), and VW Stiftung

Proper citation: Institute of Neuroinformatics (RRID:SCR_008331) Copy   

•   Source: SciCrunch Registry

http://www.epidata.dk

Sustainability plan EpiData Software has since 2000 grown from securing the principles of Epi Info V6 to an independent and documentation based system with several translations and numerous downloads. To secure continued viability organisations and governments work is being done to secure for the future, see also the license principles - the ambition is to convert the programs to open-source within few years. Contributions are used for costs of development after version 1.5 (e.g. refining of programming, enhancing speed, maintenance of website, to pay for absence from paid work to do EpiData or other developmental and promotional efforts for EpiData). About the EpiData Association EpiData Software is from EpiData Entry version 2.0 and above released by the non-profit organisation The EpiData Association Odense, Denmark (In Danish: EpiData foreningen). The association receives NO baseline budget from anyone. The association has no employees Postal adress is: The EpiData Association, att. Jens Lauritsen, Enghavevej 34, DK5230 Odense M, Denmark, Europe The body of users of EpiData form the most important part of the basis of the EpiData Association. Those who choose to register as users will be asked when desicions are to made regarding additions to the program. Needs for documentation etc. Registration is done by adding your e-mail to the Information list. Supporting members or institutions adds to the foundation and development of EpiData by securing funding to pay for the associated costs. List of donors. The board of the association is made up of the core persons developing EpiData, currently Jens M.Lauritsen and Michael Bruus in collaboration with experienced users and the Friends Of EpiData group (FoED), comprising a group of international persons wishing to support the development of EpiData Sponsor. Without support from a number of NGO''s, Universities, Regional Health Authorities and other funding bodies EpiData development would have stopped

Proper citation: EpiData Software (RRID:SCR_008485) Copy   

•   Source: SciCrunch Registry

http://www.theseed.org/DinsdaleSupplementalMaterial/

his table shows the metadata and links to sources of the data and citations associated with the publicly available metagenome sequences used in the Dinsdale, Edwards, et al., analysis of 87 different metagenomes. The links will take you to the annotated sequences in the metagenomics SEED, CAMERA, and the NCBI Short Read Archve. Please note that all metagenomes are currently available to download via the ftp links, some are available in the meta-RAST, and other links will be added as soon as they become available. Citations for individual metagenomes will also be added as and when they become available. DNA sequences for all metagenomes are avaialble via anonymous FTP. Sponsor. This project was supported by the Gordon and Betty Moore Foundation Marine Microbial Initiative, National Science Foundation grants (F.R. and D.L.V.), a Department of Commerce ATP grant (F.R.), a National Research Initiative Competitive Grant from the USDA Cooperative State Research, Education and Extension Service (B.W.), the National Institute of Allergy and Infectious Diseases, the National Institutes of Health and the Department of Health and Human Services (R.S.).

Proper citation: Metagenomes Used in The Statistical Analysis (RRID:SCR_008483) Copy   

•   Source: SciCrunch Registry