Curator Dashboard

A software repository which provides and builds open source tools for open science. rOpenSci provides packages that allow access to data repositories through the R statistical programming environment. R packages are grouped by what the tools do: acquire data, full-text of journal articles, altmetrics, data-publication, reproducibility, and data visualization.

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• SciCrunch
• 12 years ago - submitted by Kristen Jensen

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.

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• SciCrunch
• 12 years ago - submitted by Kristen Jensen

A web application and interactive computational environment where users can combine code execution, rich text, mathematics, plots, and rich media. IPython Notebook consists of two parts, the web application and plain texts. The Ipython Notebook web application is used for interactive authoring of literate computations, in which explanatory text, mathematics, computations, and rich media output may be combined. Input and output are stored in persistent cells that may be edited in-place. The plain text documents, called notebooks, record and distribute the results of the rich computations. Saved files in the notebook can be put under version control and shared with colleagues.

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• SciCrunch
• 12 years ago - submitted by Kristen Jensen

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.

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• SciCrunch
• 12 years ago - submitted by Kristen Jensen

A multi-purpose project automation tool written in Python which helps create technical documents. Dexy is a free-form literate documentation tool for writing any kind of technical document incorporating code. It provides a consistent interface to tools and scripts and keeps track of what to run, in which order, and with what parameters.

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• SciCrunch
• 12 years ago - submitted by Kristen Jensen

A software application which automatically packages up the code, data, and environment required to deploy and run Linux programs on other machines without any installation or configuration. Users can prepend any set of Linux commands with the "cde" binary, and CDE will run them and automatically package up all files accessed during execution. A package is a directory that can be compressed and delivered to any x86-Linux machine and contains all the files and environment variables required to run the original commands. After receiving the package, the user can run those same commands from within the package on any modern x86-Linux distro., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 12 years ago - submitted by Kristen Jensen

A biomaterial supply resource which collects and disseminates human heart tissue. Samples include both failing and non-failing hearts, RNA/DNA analysis, tissue staining and immunofluorescence samples.The tissue that has been flash frozen and stored at -80˚C is acquired from distinct regions of the heart such as the LV free wall, septum, and valve leaflets. Individual sample sizes are typically 100-300mg for flash frozen tissues. The DHHR also serves as a resource for assay development, target identification, and sponsored research, capable of isolating cardiomyocytes from hearts and using them for in-vitro assays such as calcium handling, enzyme activity, signalling pathways and other biochemical research activities

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• SciCrunch
• 12 years ago - submitted by Kristen Jensen

BBRB supports medical discovery and precision medicine by providing leadership, tools, and resources to the biobanking community. Provides input on policy related to biobanking and supports the availability of biospecimens for research. Develops standardized procedures for biospecimen science and research; conducts and sponsors research on the effects of biospecimen preanalytical factors; leads and supports major scientific initiatives requiring high-quality biospecimens; and supports investigations into the ethical, legal, and social issues concerning biospecimen collection and use.

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• SciCrunch
• 12 years ago - submitted by Kristen Jensen

A web-based production service resource which provides access to remote life science research labs powered by custom robotic automation. The typical Transcriptic deployment happens in three stages. Transcriptic first executes a proof-of-concept (POC) to gather important reliability and sensitivity data that will inform the handling of the project and generate validation data for the customer. Once a POC has been successfully completed, w a four-to-six week pilot study is run where the customer provides real samples at small scale. Once the process is stable, scale up occurs and a larger number of samples can be processed. Users can access results, environmental monitoring data, and all workcell actions, as well as remotely monitor all environmental parameters taking place inside the enclosed, sterile automated lab (temperature, humidity and atmospheric composition).

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• SciCrunch
• 12 years ago - submitted by Kristen Jensen

A software provider which supplies researchers with software that enables remote monitoring and management of experiments. TetraScience provides software for managing lab cameras, sensors, electrical switches, adapters, and timers. Users are notified by text or email of lab proceedings and alerts.

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• SciCrunch
• 12 years ago - submitted by Kristen Jensen

A production service resource which allows researchers to conduct experimental procedures through the cloud. Researchers can ship samples for an experiment to Emerald, then design the experiment(s) over the web using ECL software. Emerald then conducts the experiment(s) in an automated lab as specified, organizing the data into a database in the cloud. Samples are then shipped back to the lab (within a metter of days) and results can be analyze ECL's data analysis suite. Standard experiment types include but are not limited to: analytical balance readings, light microscopy, solid phase extraction, flourescence thermodynamics, RNA extraction/cDNA prep, and Western blot. Additional experiment types may be contributed.

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• SciCrunch
• 12 years ago - submitted by Kristen Jensen

An ELN (electronic lab notebook) software application which can be used to document neuroscience projects and store metadata. LabLog is meant to constitute a laboratory's long term memory for project related information. To do this, project information is stored in a central laboratory database and can be easily retrieved by searching and filtering.

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• SciCrunch
• 12 years ago - submitted by Kristen Jensen

An ELN (electronic lab notebook) software application where researchers can record and organize their data by recording, dragging, and dropping elements. Users can utilize tools and features such as image annotation, search and filter, protocol templates, and team communication. The format of the ELN is customizable and can be rearranged at any point.

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• SciCrunch
• 12 years ago - submitted by Kristen Jensen

An ELN (electronic lab notebook) software application where researchers can record and organize their data in lieu of a paper notebook. Users can store and edit texts, PDFs, spreadsheets, images, sample collections, and other types of data. LabArchives automatically backs up data and data can be accessed anywhere. Users can choose to use the professional edition of LabArhives, the classroom edition, or to purchase an enterprise license.

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• SciCrunch
• 12 years ago - submitted by Kristen Jensen

An ELN (electronic lab notebook) software application that allows researchers to organize and manage experiment tasks, protocols, and results. Users can divide experiments into tasks spread across weeks and keep track of multiple experiments and protocols using a variety of apps, such as timestamps and completion markers. Files can be stored in the Findings library and opened in a given application.

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• SciCrunch
• 12 years ago - submitted by Kristen Jensen

An open access electronic lab notebook which helps users design and organize lab experiments. Users can upload files and embed images of any type into the ELN, as well as export in PDF or zip archive into the electronic notebook. The database stores reagents, protocols, and other lab and experiment necessities for different kinds of labs. It is a PHP + MySQL application that users install on a server. After it is installed, the ELN is located in the browser.

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• SciCrunch
• 12 years ago - submitted by Kristen Jensen

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.

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• SciCrunch
• 12 years ago - submitted by Kristen Jensen

A production service resource which allows researchers to enlist the help of volunteers in projects. Researchers can build web-based projects where volunteers can assist in identification, classification, and/or characterization of specific "items" in images. An example of a project is having volunteers mark the instances when nematode worms lay eggs as part of a larger project concerning genes and behavior.

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• SciCrunch
• 12 years ago - submitted by Kristen Jensen

A collection of concise summaries of scientific articles that link back to the physical article. Users can contribute resources to the site and may choose to provide a summary; if they do not, Useful Science will do so. Summaries are then tagged with the appropriate topic. Topics that relate to everday life such as health, fitness, nutrition, and sleep are the main focus of the site.

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• SciCrunch
• 12 years ago - submitted by Kristen Jensen

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.

• Resource
• SciCrunch
• 12 years ago - submitted by Kristen Jensen