Tools   Select Another Resource Report Type

http://en.uoa.gr/

Public university in Athens, Greece that offers degree programs in health sciences, law and economics, and theology.

Proper citation: University of Athens; Athens; Greece (RRID:SCR_002607) Copy   

•   Source: SciCrunch Registry

http://pkp.sfu.ca/ojs/

Open source software made freely available to journals worldwide for the purpose of making open access publishing a viable option for more journals, as open access can increase a journal's readership as well as its contribution to the public good on a global scale. OJS assists with every stage of the refereed publishing process, from submissions through to online publication and indexing. Through its management systems, its finely grained indexing of research, and the context it provides for research, OJS seeks to improve both the scholarly and public quality of refereed research. OJS Features # OJS is installed locally and locally controlled. # Editors configure requirements, sections, review process, etc. # Online submission and management of all content. # Subscription module with delayed open access options. # Comprehensive indexing of content part of global system. # Reading Tools for content, based on field and editors' choice. # Email notification and commenting ability for readers. # Complete context-sensitive online Help support.

Proper citation: Open Journal Systems (RRID:SCR_002642) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/peptide-shaker/

Software providing a search engine independent platform for visualization of peptide and protein identification results from multiple search engines, currently supporting X!Tandem, MS-GF+, MS Amanda, OMSSA, MyriMatch, Comet, Tide, Mascot and mzIdentML. By combining the results from multiple search engines, while re-calculating PTM localization scores and redoing the protein inference, PeptideShaker attempts to give you the best possible understanding of your proteomics data.

Proper citation: PeptideShaker (RRID:SCR_002520) Copy   

•   Source: SciCrunch Registry

http://www.mementoweb.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. An extension for Chrome to see a version of a resource as it existed at some date in the past, by entering that URI in your browser and by specifying the desired date in a browser plug-in. Or you can actually browse the Web of the past by selecting a date and clicking. Whatever you land upon will be versions of Web resources as they were around the selected date. (This will only work if previous versions are available somewhere on the Web.)

Proper citation: Memento (RRID:SCR_002634) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/penncnv

A free software tool for Copy Number Variation (CNV) detection from SNP genotyping arrays. Currently it can handle signal intensity data from Illumina and Affymetrix arrays. With appropriate preparation of file format, it can also handle other types of SNP arrays and oligonucleotide arrays. PennCNV implements a hidden Markov model (HMM) that integrates multiple sources of information to infer CNV calls for individual genotyped samples. It differs form segmentation-based algorithm in that it considered SNP allelic ratio distribution as well as other factors, in addition to signal intensity alone. In addition, PennCNV can optionally utilize family information to generate family-based CNV calls by several different algorithms. Furthermore, PennCNV can generate CNV calls given a specific set of candidate CNV regions, through a validation-calling algorithm.

Proper citation: PennCNV (RRID:SCR_002518) Copy   

•   Source: SciCrunch Registry

http://www.osmicenterprises.com

A computerized, odor delivery device that can be used for basic research applications including mapping olfactory centers, cognitive / learning research, neuro-marketing among other uses. Additional products including tests for odor threshold, odor identification, odor discrimination and odor memory.

Proper citation: OEI fMRI compatible olfactometer (RRID:SCR_002507) Copy   

•   Source: SciCrunch Registry

http://liulab.dfci.harvard.edu/BINOCh/

Software that infers the identity of transcription factors used to regulate cell response to stimulus or determine a program of differentiation. It uses genome wide information on enhancer proximal nucleosome occupancy, acquired using ChIP-seq targeting enhancer related histone modifications., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026.

Proper citation: BINOCh (RRID:SCR_002778) Copy   

•   Source: SciCrunch Registry

https://github.com/grenaud/leeHom

Software program for the Bayesian reconstruction of ancient DNA fragments. The algorithm removes the adaptors and reconstructs the original DNA sequences using a Bayesian maximum a posteriori probability approach.

Proper citation: leeHom (RRID:SCR_002710) Copy   

•   Source: SciCrunch Registry

http://www.unibas.ch/

Public university in Basel, Switzerland that offers degree programs in theology, law, medicine, humanities and social sciences, science, psychology, and business and economics.

Proper citation: University of Basel; Basel; Switzerland (RRID:SCR_002699) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/pathview.html

A tool set for pathway-based data integration and visualization. It maps and renders a wide variety of biological data on relevant pathway graphs. All users need is to supply their data and specify the target pathway. Pathview automatically downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, Pathview also seamlessly integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.

Proper citation: Pathview (RRID:SCR_002732) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/glprobs/

Software implementing a simple and effective approach to improve the accuracy of multiple sequence alignment.

Proper citation: GLProbs (RRID:SCR_002739) Copy   

•   Source: SciCrunch Registry

http://www.neuro.nl

The department of Neuroscience was founded in 2001, resulting from a merger between the Physiology and Anatomy department. In 2008, the BNT department joined forces. At present we consist of about 150 people. Our research is dedicated to Plasticity and Dynamics of Sensori-Motor Systems, which we investigate at the physiological, anatomical end molecular level in 18 different research groups. We have teaching responsibilities within the whole bachelor's phase of the medical curriculum at the Erasmus MC, teaching both basic anatomy and physiology, as well as neuroscience. The department hosts its own Master of Neuroscience program. The department of Neuroscience is embedded in the ONWAR, Helmholtz, and MGC research school

Proper citation: Erasmus MC Department of Neuroscience (RRID:SCR_002737) Copy   

•   Source: SciCrunch Registry

http://www.flymine.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. Integrated database of genomic, expression and protein data for Drosophila, Anopheles, C. elegans and other organisms. You can run flexible queries, export results and analyze lists of data. FlyMine presents data in categories, with each providing information on a particular type of data (for example Gene Expression or Protein Interactions). Template queries, as well as the QueryBuilder itself, allow you to perform searches that span data from more than one category. Advanced users can use a flexible query interface to construct their own data mining queries across the multiple integrated data sources, to modify existing template queries or to create your own template queries. Access our FlyMine data via our Application Programming Interface (API). We provide client libraries in the following languages: Perl, Python, Ruby and & Java API

Proper citation: FlyMine (RRID:SCR_002694) Copy   

•   Source: SciCrunch Registry

http://www.srnt.org/

With over a thousand members, including many of the top experts on nicotine and tobacco from over 20 countries around the world, the Society for Research on Nicotine and Tobacco's mission is to stimulate the generation of new knowledge concerning nicotine in all its manifestations - from molecular to societal. The Society has the following goals: 1. To sponsor scientific meetings and publications fostering the exchange of information on the biological, behavioral, social, and economic effects of nicotine; these activities shall include basic research and research on mechanisms of action and the use of nicotine as a probe for studying nervous systems function as well as applied research on the behavioral and pharmacological aspects of tobacco use, nicotine dependence, the therapeutic uses of nicotine, and related areas. 2. To encourage scientific research on public health efforts for the prevention and treatment of cigarette and tobacco use. 3. To provide the means by which various legislative, governmental, regulatory, and other public agencies and the ethical drug industry can obtain expert advice and consultation on critical issues concerning tobacco use, nicotine dependence, and the therapeutic uses of nicotine. Membership dues will be used to plan an annual meeting, to publish a newsletter, to compile a directory, to conduct advocacy and liaison activities for nicotine research, and to begin work on professional publications such as a journal. Though the Society will meet at least once per year in North America and will be incorporated in the United States, the intent is to be international in scope, with co-sponsorship of meetings in other countries and active recruitment of members outside the United States. By clicking on the various links on the website you can gain access to further information about the society, its publications, activities and membership. In 2004, the Society for Research on Nicotine and Tobacco celebrated the tenth anniversary of its founding. During its first decade, the Society grew from around 100 to over 900 members, sponsored well-attended annual meetings and highly-influential satellite conferences to promote research, provided timely electronic and print services to increase the flow of information, and founded a new peer-reviewed journal (Nicotine and Tobacco Research: The Journal of SRNT) to facilitate communication of scientific advances. The record documents considerable progress in meeting the objective of the Society to stimulate new knowledge about nicotine in all its manifestations. As part of SRNT's Decade One celebration, two projects were developed to commemorate its achievements and help preserve its collective memory. The first is an article by two past presidents, Ovide Pomerleau and John Hughes, entitled With a little help from its friends: A brief history of the Society for Research on Nicotine and Tobacco, published in the Societys journal, Nicotine and Tobacco Research. The second is a series of e-interviews with each of SRNTs first ten presidents. A brief structured interview was designed, and the former presidents were invited to respond in writing to each question in as little or as much detail as desired. An open-ended question was provided at the end to allow for more free-form commentary. The results of this effort can be accessed via the links below.

Proper citation: Society for Research on Nicotine and Tobacco (RRID:SCR_002753) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/rBiopaxParser.html

A software package that provides a comprehensive set of functions for parsing, viewing and modifying BioPAX pathway data within R. At the moment BioPAX level 2 and level 3 are supported.

Proper citation: rBiopaxParser (RRID:SCR_002744) Copy   

•   Source: SciCrunch Registry

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

Software to cluster genes based on Poisson or Negative-Binomial model for RNA-Seq or other digital gene expression (DGE) data.

Proper citation: MBCluster.Seq (RRID:SCR_005079) Copy   

•   Source: SciCrunch Registry

http://www.biomedcentral.com/1471-2105/13/189

An algorithm to use optical map information directly within the de Bruijn graph framework to help produce an accurate assembly of a genome that is consistent with the optical map information provided. AGORA takes as input two data structures: OpMap ? an ordered list of fragment sizes representing the optical map; and Edges ? a list of de Bruijn graph edges with their corresponding sequences.

Proper citation: AGORA (RRID:SCR_005070) Copy   

•   Source: SciCrunch Registry

https://github.com/AlexeyG/GRASS

A generic algorithm for scaffolding next-generation sequencing assemblies.

Proper citation: GRASS (RRID:SCR_005071) Copy   

•   Source: SciCrunch Registry

http://www.bioinf.boku.ac.at/pub/MapAl/

A software tool for RNA-Seq expression profiling that builds on the established programs Bowtie and Cufflinks. Allowing an incorporation of ''gene models'' already at the alignment stage almost doubles the number of transcripts that can be measured reliably.

Proper citation: MapAl (RRID:SCR_004938) Copy   

•   Source: SciCrunch Registry

http://www.open.ac.uk/

Public research university and the largest university in the UK for undergraduate education. The majority of the OU's undergraduate students are based in the United Kingdom and principally study off-campus; many of its courses can also be studied anywhere in the world.

Proper citation: Open University; Milton Keynes; United Kingdom (RRID:SCR_004931) Copy   

•   Source: SciCrunch Registry