Digital tools for researchers

At the bench and in the office

Here is a collection of tools that help researchers in their everyday tasks. Go to Lab and project management, for tools that help manage stocks and equipment's in the lab as well as project management tools for research. You’ll also find a selection of Electronic lab notebooks developed with academic researchers in mind first. Many others are available elsewhere. Outsourcing experiments is increasingly common in academic research, in part thanks to several sites that are making it easier and cheaper. Platforms to Find and share samples help you disseminate and find materials and biological samples. Under Protocol repository, you will find a collection of publicly accessible resource for experimental protocols. Work with code gathers tools designed to make the coder’s life easier and Work with data tools to generate and analyze data sets, including many R-based tools.

Lab and project management

• 1degreebio – Reagent marketplace.
• Antibody Registry – Gives researchers a way to universally identify antibodies used in in the course of their research.
• Asana – Keeps your team organized, connected, and focused on results.
• Biocompare – Find products, read reviews and hear about the latest technological developments.
• ELabInventory – Web-based laboratory inventory management system designed for life science research laboratories
• LabCritics – Provides researchers with a trust-able source of lab equipment reviews and comparisons.
• LabGuru – Supports day to day activities of a research group, from vision to execution, from knowledge to logistics.
• Life technologies Lab Management Tool – Management tool for lab equipment and services.
• Open Science Framework – Gathers a network of research documents, a version control system, and a collaboration software.
• Quartzy – A free and easy way to manage your lab.
• Quip – Combines chat, documents, spreadsheets, checklist, and more to collaborate on any device.
• StrainControl – Lab management tools that allows you to organize strains, plasmids, oligos, antibodies, chemicals and inventorie.
• Synapse – Platform to support open, collaborative data analysis for clear, reproducible science

Electronic lab notebook

• Docollab – Helps you manage your scientific research, collaborate with your colleagues and publish your findings.
• elabftw – Electromic lab notebook made by researchers, for researchers, with usability in mind.
• Evernote – A place to collect inspirational ideas, write meaningful words, and move your important projects forward.
• Findings App – Lab notebook app that allows to organize your experiments, keep track of results, and manage your protocols.
• Hivebench – Hosted numeric laboratory notebook tool to manage protocols, experiments and share them with your team.
• Journal Lab – A community of scientists who share open summaries and peer review of published articles. (blog post)
• LabArchives – Web-based product to enable researchers to store, organize, and publish their research data.
• Labfolder – Simple way to document your research and to organize your protocols and data. (blog post)
• LabGuru – Supports day to day activities of a research group, from vision to execution, from knowledge to logistics.
• Laboratory Logbook – Document projects running in a lab and manage experimentally obtained data and its metadata.
• Sumatra – Automated electronic lab notebook for computational projects.

Outsourcing experiments

• Emerald Cloud Lab – A web-based life sciences lab, developed by scientists for scientists.
• ScienceExchange – Marketplace for shared lab instrumentation. (blog post)
• TetraScience – Allows you to monitor & manage your experiments from anywhere.
• Transcriptic – A remote, on-demand robotic life science research lab with no hardware to buy or software to install.
• Zombal – Connects the scientific community globally for scientific outsourcing

Find and share samples

• Addgene – Plasmid sharing platform
• Antibody Registery – Gives researchers a way to universally identify antibodies used in in the course of their research.
• Biospecimens – Platform for biospecimen-based research.
• Duke human heart - Repository for cardiovascular research scientists, including tissues samples and information.
• ELabInventory – Web-based laboratory inventory management system designed for life science research laboratories.
• Nanosupply – Platform facilitating sourcing and sharing of advanced materials for research and education.
• Sample of Science – Peer-Sharing Platform for Scientific Samples. (blog post)

Protocol repository

• SciVee – Science video sharing platform that includes protocols.
• Benchfly – Video protocols and video platform for scientists.
• Benchling – Life science data management and collaboration platform, where you can create, find, and discuss protocols.
• IPOL journal - Research journal of image processing and image analysis with algorithm descriptions and its source code.
• MyExperiment – Share workflows and in silico experiments.
• OpenWetWare – Share information, know-how, wisdom, and protocols among researchers working in biological fields.
• Pegasus – Platform that help workflow-based applications execute.
• Protocols – Crowdsourced universal protocol repository. (blog post)
• Protocol online – A curator of protocols contributed by researchers arounds the world.
• Scientific Protocols – Share scientific protocols using the GitHub platform.

Work with code

• CDE Tool - Deploy and run your Linux programs on other machines without any installation or configuration.
• Dexy – Helps your code to speak for itself with beautiful syntax highlighting.
• GitLab – A git repository management, code reviews, issue tracking and wiki’s all in one platform.
• iPython notebook – Interactive computational environment that allows code execution, text, mathematics, plots, and rich media.
• Kepler – Helps create, execute, and share models and analyses across scientific and engineering disciplines.
• Mercurial – Control management tool with distributed source, giving each developer a local copy of the development history.
• nanoHUB – Centralized platform for computational nanotechnology research, education, and collaboration.
• ROpenSci – Packages that allow access to data repositories through the R statistical programming environment.
• Sweave – Allows to embed the R code for complete data analyses in latex documents
• System in Cloud – Platform, enabling clients to rapidly draw and execute data-flow diagram that run in cloud.

Work with data

• Benchling – Life science data management and collaboration platform.
• Galaxy Project – Web-based platform for data intensive biomedical research.
• GenePattern – Genomic analysis platform that provides access to hundreds of genomics tools.
• GenomeCompiler – Genetic design platform allowing researchers to manipulate and design everything from single genes to entire genomes.
• Kaggle – Patform for data prediction competitions.
• Kitware – Advanced software solutions and services for data intensive R&D
• mloss – Machine learning open source software.
• MyExperiment – Share workflows and in silico experiments
• nanoHUB – Centralized platform for computational nanotechnology research, education, and collaboration.
• Pegasus – Platform that help workflow-based applications execute.
• Plotly – Online tool to graph and share data.
• ROpenSci – Packages that allow access to data repositories through the R statistical programming environment.
• Statcrunch  – Provides data analysis via the Web.
• Sumatra – Automated electronic lab notebook for computational projects
• SURF In context – Navigate through RDF relations in a smooth and understandable way.
• Sweave – Allows to embed the R code for complete data analyses in latex documents.
• Synapse – Platform to support open, collaborative data analysis for clear, reproducible science.
• System in Cloud – Platform, enabling clients to rapidly draw and execute data-flow diagram that run in cloud.
• Tableau – Easily and quickly analyze and present data and share insights.
• Taverna – A suite of tools used to design and execute scientific workflows.
• VisTrails – Scientific workflow and provenance management system that supports data exploration and visualization.
• Wakari – Web-based python data analysis.
• WebPlotDigitizer – Web based tool to extract data from plots, images, and maps. (blog post)
• Wings – Semantic workflow system that assists scientists with the design of computational experiments.
• Wolfram Alpha – Web-based tools for scientific calculations.
• World Map – Allows users to explore, visualize, edit, collaborate with, and publish geospatial information.

Fundraising/Grant writing

• Grant Forward – Search engine for research grants.
• Pivot COS – A database which includes funding opportunities from all disciplines.