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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
https://www.peerageofscience.org
A peer review service resource which allows researchers to dictate the time constraints in which their manuscripts are peer reviewed. Authors submit their manuscript to Peerage of Science before submitting to any journal and decide the deadlines for the four stages of the process (which are "Submission and Reviews," "Peer-review-of-peer-review," "Manuscript revision upload or withdrawal for re-submission," and "Final evaluation of the revised manuscript"). Once submitted, any qualified, non-affiliated Peer can choose to review the manuscript. The peer reviews are peer reviewed and are also available to all subscribing journals with automated event tracking. Authors may accept a direct publishing offer from a subscribing journal, or choose to export the peer reviews to any journal of their choice.
Proper citation: Peerage of Science (RRID:SCR_014007) Copy
A web application which allows users to record, organize, and manage lab equipment online. Instrument Management provides tools to view service history and field service reports, request service or service quotes online, monitor warranty or contract statuses, and view instrument details.
Proper citation: Life Technologies Instrument Management (RRID:SCR_013970) Copy
International, curated, digital repository that makes the data underlying scientific publications discoverable, freely reusable, and citable. Particularly data for which no specialized repository exists. Provides the infrastructure for, and promotes the re-use of, data underlying the scholarly literature. Governed by a nonprofit membership organization. Membership is open to any stakeholder organization, including but not limited to journals, scientific societies, publishers, research institutions, libraries, and funding organizations. Most data are associated with peer-reviewed articles, although data associated with non-peer reviewed publications from reputable academic sources, such as dissertations, are also accepted. Used to validate published findings, explore new analysis methodologies, repurpose data for research questions unanticipated by the original authors, and perform synthetic studies.UC system is member organization of Dryad general subject data repository.
Proper citation: Dryad Digital Repository (RRID:SCR_005910) Copy
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
A video resource containing short, scientific videos which can be browsed or searched for. The videos are based on published papers, talks or posters. It is free to use and disseminates research findings to the world wide web. SciVee enables researchers to combine video with documentation and data in a media rich format, enhancing journal articles with pubcasts by linking and synchronizing video explanations to their published text. Similarly, video summaries can be associated and synchronized with scientific posters to create postercasts highlighting the key finding of the research.
Proper citation: SciVee (RRID:SCR_004837) Copy
http://cchum-kvm-execandshare.in2p3.fr/CompanionSite/
A database and storage service resource that allows researchers to create a companion website, a website which allows people to run the computer codes associated with a scientific publication. Users upload or paste data, choose the value of the parameters, and click on the Exec&Share button. All calculations are done on a dedicated cloud computer and are automatically displayed to the user. It is also possible to only make the code downloadable, but not executable. In that case, users can download the code and run it on their own computer. Companion websites can currently be made from a code written in R, MATLAB©, C++, Fortran, and Rats.
Proper citation: Exec&Share (RRID:SCR_014009) Copy
An online resource which helps researchers manage and organize labs and experimental results by supplying molecular biology software tools for experimental design and data analysis. Benchling provides tools for functions such as primer design and colony counting as well as CRISPR guide design and automated Gibson and Golden Gate cloning. Users can take notes in line with data, link data across entries, keep files and data in one place, and manage and keep track of team progress. An enterprise version of Benchling is available for scientists working within an organization with additional administrative, compliance, and security protocols.
Proper citation: Benchling (RRID:SCR_013955) Copy
An access service resource which serves as a global open access hub for the sharing and licensing of Biological Research Materials and related technologies with researchers. Biomedical researchers from research institutions and industry can connect with Technology Transfer Offices owning proprietary Biological Research Materials or rights to relevant technologies. Users can also search BioMedUSA's aggregated resources, such as biorepositotires and biologicals to share/license, for materials and technologies.
Proper citation: BiomedUSA (RRID:SCR_013956) Copy
An on-going project and collaboration tool where biomedical researchers can access to expertise and related resources across institutions, regardless of local platforms and tools. Users can work with participating institutions in order to connect to their existing research networking tools. Biomedical institutions that wish to participate must have a mature, deployed research networking tool and can commit resources to assessments.
Proper citation: DIRECT2experts (RRID:SCR_013958) Copy
https://developers.google.com/chart/
A web application which allows users to create data visualizations using JavaScript that can be embedded in a web page. Users can load some Google Chart libraries, list the data to be charted, select options to customize their chart, and create a chart object with a personally chosen id. Then, in the web page, users create a
Proper citation: Google Charts (RRID:SCR_014010) Copy
https://www.trelliscience.com/#/site-home
A collaboration tool designed specifically for scientists as a place to collaborate and engage in activities with others. Users can create and manage a professional profile, meet new people and build their professional network, find the latest news and updates in science, participate in online conversations, upload and manage documents, and host a journal club, a live chat-based Q&A, or a presentation series.
Proper citation: Trellis (RRID:SCR_013819) Copy
A web application which allows users to collaboratively write documents and books with version control and revision history. Users can write in plain text or with Markdown and invite others to collaborate on their work. Math equations can be written with LaTeX or MathML with MathJax. eBooks can be downloaded and compiled into forms such as PDF, ePub, Word, and HTML . Works can be made public or kept private.
Proper citation: Penflip (RRID:SCR_014004) Copy
A software application which assists scientists with designing computational experiments. WINGS is a semantic workflow system which incorporates semantic constraints about datasets and workflow components into its workflow representations. The workflow system has an open modular design and can be easily integrated with other existing workflow systems and execution frameworks to extend them with semantic reasoning capabilities. WINGS also allows users to express high-level descriptions of their analysis goals, and assists them by automatically and systematically generating possible workflows that are consistent with that request. In cases where privacy or off-line use are important, WINGS can submit workflows in a scripted format for execution in the local host. It uses Pegasus or OODT as the execution engine for large-scale distributed workflow execution.
Proper citation: WINGS (RRID:SCR_013997) Copy
http://www.tableau.com/products/desktop
A software application which utilizes drag-and-drop to create data visualizations of various formats. Users can collaborate on and discuss data and graphs that can be created from spreadsheets, databases, and big data sources. Three versions of Tableau Desktop are available: Tableau Server, Tableau Online, and Tableau Reader.
Proper citation: Tableau Desktop (RRID:SCR_013994) Copy
A database where researchers and editors can read and post reviews and ratings of scientific journals and their publishing processes. Efficient journals get credits for their efforts to improve their review process and the way they handle manuscripts, while less efficient journals are stimulated to put energy in better organization. Researchers can search for a journal with a speedy review procedure and have their papers published earlier. Editors get the opportunity to compare their journal's performance with that of others and to provide information about their journal at our website.
Proper citation: SciRev (RRID:SCR_014016) Copy
http://www.liberatingresearch.org
A repository which hosts and archives original and edited scientific papers. Scientists can post their academic manuscripts on Libre, where they can find reviewers who will formally evaluate the manuscripts. Evaluated works are posted alongside the original manuscript with reviewers' identities disclosed and the work they edit given its own DOI. Users can post additional updated versions of their work to Libre or send their papers to journals. Papers and reviews are rated by other scientists, and from these Libre creates holistic indeces listing the best rated writers and reviewers.
Proper citation: Libre (RRID:SCR_014018) Copy
A production service resource which transforms scientific articles into infographics. In order to make an infograph, users must submit a package to DrawScience containing a scholarly article(s) to base the infographic on, a summary of the rationale and conclusions of the research, and definitions for 5 or less terms necessary to understand the research. Users may also make an infographic which will be attributed to them.
Proper citation: DrawScience (RRID:SCR_013967) Copy
A service resource which allows peer reviewers to record and showcase the peer reviews they have completed, both those that led to publication and to rejection. Peer reviews can be recorded on Publons by forwarding review receipts from journals to the site. The merit of reviewers is accrued by pre- and post-publication peer review, discussion papers in Publons, and comments on or endorsment of the contributions of other reviewers. Reviewers may publish their own reviews so long as the reviewed manuscript is published and the review policies of the journal allow for it. Users can choose what personal information is displayed and easily export their profile in a format suitable for inclusion in promotion and funding applications.
Proper citation: Publons (RRID:SCR_014020) Copy
A software application which provides Git repository management with fine grained access controls, code reviews, issue tracking, activity feeds, wikis, and continuous integration. Four different versions are available, each with different packaging pricing: Community edition, Enterprise edition, Continuous integration, and GitLab.com.
Proper citation: GitLab (RRID:SCR_013983) Copy
A software application which provides distributed source control management for projects. Using Mercurial, each developer has a local copy of the project development history. Mercurialhas a user friendly interface, is written mostly in Python, and works independently of network access or a central server. Functionality can be increased using extensions, either by downloading them or writing new ones.
Proper citation: Mercurial (RRID:SCR_013985) Copy
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