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https://www.writelatex.com

A collaboration tool which allows users to edit and publish scientific articles and papers. Overleaf utilizes the convenience of an easy-to-use WYSIWYG manuscript editor with real-time collaboration and structured, fully typeset output produced automatically. Authors can publish immediately and directly to their journal of choice while publishers can reduce their editorial and review turnaround times with powerful change tracking, commenting, and project lifecycle management features. It was formerly known as writeLaTex but changed its name to Overleaf in 2015.

Proper citation: Overleaf (RRID:SCR_003232) Copy   

•   Source: SciCrunch Registry
  

http://r3cseq.genereg.net/Site/index.html

An R/Bioconductor package to identify chromosomal interaction regions generated by chromosome conformation capture (3C) coupled to next-generation sequencing (NGS), a technique termed 3C-seq. It performs data analysis for a number of different experimental designs, as it can analyze 3C-seq data with or without a control experiment and it can be used to facilitate data analysis for experiments with multiple replicates. The r3Cseq package provides functions to perform data normalization, statistical analysis for cis/trans interactions and visualization in order to help scientists identify genomic regions that physically interact with the given viewpoints of interest. This tool greatly facilitates hypothesis generation and the interpretation of experimental results.

Proper citation: r3Cseq (RRID:SCR_003198) Copy   

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http://lalashan.mcmaster.ca/theobio/projects/index.php/WorkingWiki

Free software extension for MediaWiki that makes a wiki into an environment for collaborating on publication-quality manuscripts and software projects. It allows wiki users to work together on anything that can be done by using UNIX commands to transform textual source code into output. Researchers can use it to collaborate on programs written in R, python, C, or any other language, and there are special features to support easy work on LaTeX documents. It develops the potential of the wiki medium to serve as a combination collaborative text editor, development environment, revision control system, and publishing platform. Its potential uses are open-ended - its processing is controlled by makefiles that are straightforward to customize - and its modular design is intended to allow parts of it to be adapted to other purposes.

Proper citation: WorkingWiki (RRID:SCR_003231) Copy   

•   Source: SciCrunch Registry
  

https://www.fitzgerald-fii.com

Commercial organization that supplies antibodies, proteins, ELISA kits, serum, and plasma to the research community.

Proper citation: Fitzgerald Industries International (RRID:SCR_003237) Copy   

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https://sites.google.com/site/bctnet/datasets

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023. This site has a collection of cortical connectivity datasets and modeling software components that can be downloaded and used for modeling of cortical circuits. The toolbox combines Matlab functions and neuroanatomical data sets useful in the analysis of structural or functional brain networks. Several people have made contributions and if you wish to contribute yourself with a new function or set of functions please contact osporns_at_indiana.edu.The following is a collection of commonly used large scale cortical connectivity data sets compiled from tract-tracing studies. Hence nodes represent cortical areas and links represent large cortico-cortical tracts. * macaque71.mat (BD network). Macaque cortical connectivity: 71 nodes 746 links. Reference: Young (1993). Contributor: OS. Used in e.g. Sporns (2002). * fve30.mat; fve32.mat (BD networks). Two version the macaque visual cortex. fve30.mat: 30 nodes 311 links. fve32.mat: 32 nodes 320 links. Reference: Felleman and van Essen (1991). Contributor: OS. Used in e.g. Sportns et al. (2000) Sporns and Kotter (2004). * macaque47.mat (BD network). Large scale cortico-cortical connectivity matrix of the visual and sensorimotor areas in the macaque. 47 nodes; 505 links. Used in e.g. Honey et al. (2007). Contributor: RK. * cat.mat (WD networks). Connection matrices of cat cortex. CIJall contains all cortical and thalamic areas: 95 nodes 2126 links. CIJctx contains only 52 cortical areas: 52 nodes 820 links. Reference: Scannell et al. (1999). Contributor: OS. Used in e.g. Sporns and Zwi (2004) Sporns and Kotter (2004). * DSIhumanctx.mat (WU networks).

Proper citation: Cortical connectivity data sets (RRID:SCR_003190) Copy   

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https://www.assays.co.il

Commercial organization that provides services for assay development, research histopathology, and early stage project consultation.

Proper citation: Smart Assays (RRID:SCR_003195) Copy   

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https://webmaker.org/

A Mozilla project to teach and enable users on how to create on the web. Their tools, events and teaching guides allow webmakers to create the content that makes the web great and understand how the web works. They've built everything so you can see how it works, take it apart and remix it

Proper citation: Webmaker (RRID:SCR_003227) Copy   

•   Source: SciCrunch Registry
  

http://www.mged.org/mage-tab/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 27,2023. A simple tab-delimited, spreadsheet-based format which will become a part of the MAGE microarray data standard that can be used for annotating and communicating microarray data in a MIAME compliant fashion. MAGE-TAB will enable laboratories without bioinformatics experience or support to manage, exchange and submit well-annotated microarray data in a standard format using a spreadsheet. The MAGE-TAB format is self-contained, and does not require an understanding of MAGE-ML or XML.

Proper citation: MAGE-TAB (RRID:SCR_003222) Copy   

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http://www.fged.org/projects/minseqe/

The Minimum Information about a high-throughput nucleotide SEQuencing Experiment that is needed to enable the unambiguous interpretation and facilitate reproduction of the results of the experiment. By analogy to the MIAME guidelines for microarray experiments, adherence to the MINSEQE guidelines will improve integration of multiple experiments across different modalities, thereby maximising the value of high-throughput research. The five elements of experimental description considered essential when making data available supporting published high-throughput sequencing experiments are as follows: # The description of the biological system, samples, and the experimental variables being studied # The sequence read data for each assay # The "final" processed (or summary) data for the set of assays in the study # General information about the experiment and sample-data relationships # Essential experimental and data processing protocols

Proper citation: MINSEQE (RRID:SCR_003221) Copy   

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http://www.w3.org/community/openannotation/

Community group working towards a common, RDF-based, specification for annotating digital resources. The effort began by trying to reconcile two proposals: the Annotation Ontology (http://code.google.com/p/annotation-ontology/) and the Open Annotation Model (http://www.openannotation.org/spec/beta/ ). Initially, editors of these proposals collaborated to devise a common draft specification that addresses requirements and use cases that were identified in the course of their respective efforts. This draft became available for public feedback and experimentation in the second quarter of 2012. The final deliverable is a specification, published under an appropriate open license, that is informed by the existing proposals, the common draft specification, and the community feedback.

Proper citation: W3C Open Annotation Community Group (RRID:SCR_003226) Copy   

•   Source: SciCrunch Registry
  

http://sobekrepository.org/

Digital repository software written in C# / ASP.net for powering digital libraries in a Windows server environment. Standards-based repository keeps all files in METS/MODS packages. Several related applications are available as well and the libraries can work independently as great digital library resources. SobekCM allows users to discover online resources via semantic and full-text searches, as well as a variety of different browse mechanisms. For each digital resource in the repository there are a plethora of display options, which may be selected by an appropriately authenticated use. This repository includes online metadata editing and online submissions in support of institutional repositories.

Proper citation: SobekCM (RRID:SCR_003225) Copy   

•   Source: SciCrunch Registry
  

http://146.20.110.164/about/

Tools for researchers to connect their data, code and computational methods to their published or soon to be published research in a convenient and easily citeable form. ResearchCompendia provides the tools to publish digital scholarly objects by hosting data, code, and methods in a form that is accessible, trackable, and persistent. They provide hosting and computational cloud resources for all researchers. Data and code should be citable and linked to the original publication.

Proper citation: ResearchCompendia (RRID:SCR_003223) Copy   

•   Source: SciCrunch Registry
  

http://creskolab.uoregon.edu/stacks/

A software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. It was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography.

Proper citation: Stacks (RRID:SCR_003184) Copy   

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http://www.ncbi.nlm.nih.gov/dbvar/

Structural variation database designed to store data on variant DNA > / = 1 bp in size from all organisms. Associations of defined variants with phenotype information is also provided. Users can browse data containing number of variant cells from each study, and filter studies by organism, study type, method and genomic variant. Organisms include human, mouse, cattle and several additional animals.

Proper citation: dbVar (RRID:SCR_003219) Copy   

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http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/

Software tool for finding the minimum free energy hybridization of a long and a short RNA. The hybridization is performed in a kind of domain mode, i.e., the short sequence is hybridized to the best fitting part of the long one. The tool is primarily meant as a means for microRNA target prediction.

Proper citation: RNAhybrid (RRID:SCR_003252) Copy   

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http://cal.tongji.edu.cn/PlantLoc/index.jsp

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4,2023. An accurate web server for predicting plant protein subcellular localization by substantiality motif.

Proper citation: PlantLoc (RRID:SCR_003138) Copy   

•   Source: SciCrunch Registry
  

http://www.stereologyresourcecenter.com/

A company of professionally trained stereologists, bioscientists, computer engineers, educators, and support personnel that provides comprehensive neurostereology products and services to the global bioscience community. These products and services include: stereology and image analysis software, digital imaging technology, turnkey stereologer solutions, comprehensive stereology and image analysis/image processing software, professional contract services, neurostereology workshops, basic stereology courses, and online stereology webinars. The Center also offers tissue processing (sectioning, staining, slide preparation) and stereology data collection services. Researchers may use equipment and facilities to complete projects with full confidentiality and according to Good Laboratory Practices guidelines.

Proper citation: Stereology Resource Center (RRID:SCR_003137) Copy   

•   Source: SciCrunch Registry
  

http://www.brc.riken.jp/inf/en

RIKEN BRC contributes to advancement of life science research by collecting, preserving and distributing biological resources such as experimental animals, experimental plants, cultured cell lines, genetic materials (DNA), and associated bioinformatics. The RIKEN BRC develops novel bioresources to promote scientific research and new technologies to increase the value of bioresources, and also to implement effective procedures for the preservation, quality control and usage of bioresources. The RIKEN BRC is working closely with institutions in Japan and abroad.

Proper citation: RIKEN BioResource Center (RRID:SCR_003250) Copy   

•   Source: SciCrunch Registry
  

http://talkbank.org/

Databases of transcript and media data collected from conversations with adults and older children to foster fundamental research in the study of human and animal communication. Conversations with children are available from CHILDES. All of the data is transcribed in CHAT and CA/CHAT formats. Databases of the following types are included in the collection: Aphasia patient speech, Child speech, Study of Phonological Development, Conversation Analysis, and Bilingualism and Second Language Acquisition. TalkBank will use these databases to advance the development of standards and tools for creating, sharing, searching, and commenting upon primary materials via networked computers.

Proper citation: TalkBank (RRID:SCR_003242) Copy   

•   Source: SciCrunch Registry
  

http://nmrml.org/cv/

Ontology for describing NMR experiments and acquisitions.

Proper citation: nmrCV (RRID:SCR_003247) Copy   

•   Source: SciCrunch Registry