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Scolary helps you to find the right tool for your workflow

It has been a while since the last update of Connected researchers. Life makes it hard for me to keep up with this site while managing a research group and a young startup. I very much will welcome help by the way! Regardless, I am keeping the site very much alive because of the strong interest from the scientific community to discover digital tools that can help them do Science better.

Luckily, Connected Researcher is not alone in this effort. Scolary being the latest. Since I think any effort making our lives as researchers easier is worth publishing. So here you go:

Scolary is a free and open compendium of software tools for the science and research community. On Scolary, you will find a growing collection of products that can improve your current workflow, served by the scientific community itself.

There are a few ways to discover tools on Scolary. Worflows are compilations of tools other scientists have put together for you. You can try out different workflows to see which works best for you. You can simply use the “discover” function and search your way into the database. Or you can explore the tools via pre-set categories, similar to what you will find on Connected Researchers (planning, exploring, analyzing..). 

Scolary will work best with the use and input from us researchers and from tool makers. So have a look! And good luck to Scolary!

12 new digital tools added to the list

In no particular order, here come a dozen new tool added to the list of digital tools for researchers that I would encourage you to explore. You will find a mix of electronic lab notebooks, writing tools, lab project management platforms, literature search engines, and more!

  • How Can I Share It – Find information and tools to ensure your articles can be shared with your colleagues quickly and easily.
  • Code Ocean – Cloud-based computational platform which provides a way to share, discover and run published code.
  • Authorcafe – Authoring and Publishing Services platform for scholarly writing.
  • antYbuddY – An independent antibody review platform and supporting peer-to-peer forum.
  • Editorlookup – Search tool to help find scientific professionals for academic tasks, such as editors and reviewers for scientific manuscripts.
  • Ref-n-Write – Microsoft Word Add-in that helps you improve your English writing skills.
  • LiveLabSpace – Collaborative research tool that lets you plan experiments, replicate outcomes and generate research papers.
  • Thinkable – Platform to mobilize knowledge and fund breakthrough ideas.
  • Labspace – A collaborative electronic lab notebook for research teams including notebook, protocols, materials.
  • Researcher App – Browse and filter papers from hundreds of journals on your mobile device.
  • SciFlow – A digital publication platform for researchers.
  • Meta – Innovation in the exploration of papers and authors.

As always, if you have discovered a new digital tool that is not in the list, or you have developed a new tool yourself, feel free to contact me so I add it to the list.

Research done more collaboratively with LiveLabSpace

Ask any researcher and he/she will tell you that you cannot do much without collaborations. Often, academic collaborations will start after meeting someone at a conference, or perhaps because you know someone down the hall with the right expertise. This type of ad hoc interactions limits the size of the collaborative networks that researchers engage with often rather small. And with less diversity of expertise and opinions, investigators (and especially the younger ones) are more likely to start less ambitious and risky projects.

Citizen science platforms where anyone can join to help with research projects have been gaining traction over the past few years. But the same approach could be also applied to scientific projects opened by researchers for other researchers. This way, ambitious research questions could be formulated by research groups big and small or even directly by research funders and industry and welcome contributions from the international scientific community. Anyone with proper accreditation or references could then contribute to the project and get proper recognition for solving part of the questions.

This year, Simon Bond has released LiveLabSpace, an online platform that could help start tackling this exact problem. LiveLabSpace is a cloud-based platform that helps manage collaborative research projects. Through its friendly graphic interface, project managers can define various research questions and tasks that need to be addressed. Then, every collaborator can upload data, write descriptions and comments about their results and the results of others. Of course, the projects do not necessarily need to be made public. Private projects can make good sense for the large-scale international project that already counts many participants or project with sensitive confidential information.

Other platforms like the Open Science Framework are also attempts at bringing scientists to collaborate on a common virtual space. But what is the difference between these platforms and an electronic lab notebook (ELN)? In my opinion, ELNs and collaborative research platforms are not so different and will eventually merge into unique platforms. At this time, tools such LiveLabSpace put the focus on project management, providing the information you need to track the history of the project, to get an overview of the results, and take appropriate decisions to drive the project forward. At this time, these collaborative platforms do not truly allow to go into the detail of single experiments like ELN can.

I have not met anyone in my academic network using such tools yet. My guess is that user-friendliness is a key issue. It is, however, much more common for users to recreate their own equivalent cloud-based workspace using a combination of tools, such as share cloud storage space (Google Drive, Dropbox…) combined with collaborative writing tools (Word online, Google docs, Overleaf) and communication tools (Skype, Hangout, Slack…). Obviously, these have their limitations and an integrated system dedicated to scientific projects could potentially make a much better option. For instance by standardizing the tools used by the collaborators and making it easy to open projects to external contributors. Let’s see how LiveLabSpace does! You can start now with free public projects without needing to register. And feel free to provide feedback to its creator.

Electronic Lab Notebooks explained

Simon Bungers, the founder, and CEO of Labfolder has just released a rather comprehensive guide about Electronic Lab Notebooks (ELNs). The motivation for Labfolder is to make sure researchers (and administrators) understand the very concrete problems ELNs are solving and how our research work can be made more efficient by using such tools. The article refers to concrete anecdotes that illustrate the usefulness of ELNs and helps you define your needs so you can find the most suitable ELN for your laboratory. Also included in the article are comparisons between a few of Labfolder’s ELN competitors that might help you in your search for the ELN that best suits you.

The guide is very much worth having a look if you ever wondered about Electronic Lab Notebook.  The post is split into the following sections:

  1. Introduction
  2. Is there really a need for a digital solution?
  3. What even the most basic ELN should do
  4. Features and structural considerations for teams
  5. Compliance, Data Governance & IP Protection
  6. App integrations & Open API
  7. Final Remarks

Insights in the digital science industry

Digital science startups (of which you can find a long list here) are playing a major role in the development of the research ecosystem of tomorrow. They are the creators of digital tools developed with researchers in mind, and that are redefining how researchers communicate with each other and society, and how research is conducted, analyzed, and evaluated.

With the development of cloud technologies, the number of digital science companies has grown rapidly over the past 10 years. I have had the opportunity to mention some of this in a report I wrote in 2015 for the European Commission. Digital science companies have emerged, typically founded by researchers frustrated with some aspect of academic research. The digital science industry is increasingly being funded by publishers that are realising they must evolve their business model away from publishing and towards innovative services for researchers (see figure below).

Elsevier’s investments in digital science companies.  The figure is from the excellent 101 Innovations in Scholarly Communication project https://innoscholcomm.silk.co/page/Elsevier

But although the importance of digital science companies is now rather clear, there is limited data available about them. We launched our Digital Science Industry survey with the goal to have a clearer picture of what the digital science industry looks like. What type of organizations is this emerging community formed of? How well are they doing? How do its actors see the future? And how can Connected Researchers and others like LabWorm.com alike help? This post summaries the responses of the 42 digital science companies that responded to the survey.

We first wanted to know who the participants were. We will not disclose the name of the companies that chose to identify themselves, but will give an overview of of their main characteristics.

Continue reading

Update of the list of digital tools for researchers.

Here is quick update of the list on digital tools for researchers with a few additions. I am also finalising the writeup of the results from the digital science industry survey that was launched a few months back. Be on the lookout for that.

As always, I am more than happy to consider any tools suggested for the list. Contributions in the form of reviews, comments, tutorial are also more than welcome.

Collaborative writing tools

  • Write – Distraction-free text editor for writing productivity.

Find and share data and code

  • Deveo – Free, private Git, Mercurial, and SVN repository management platform.

Search engines and curators

  • Delvehealth – A data collection of global clinical trials, clinical trial investigator profiles, publications and drug development pipelines.


  • Animate Science – Helps scientists get their work noticed by their peers and the general public using visual media.

Work with data

  • OMICtools –  A manually curated metadatabase of genomics, transcriptomics, proteomics and metabolomics.

Connected Researchers Update

checklist-1402461_640-1The survey we are running on digital science startups will soon come to an end. We have nearly 40 participants at the moment, which should provide us with a good overview of what digital science companies can look like. We will post the results on this blog in November. But if you are digital science tool developer, it is still time to participate!!

We also have updated the list of digital tools for researchers with 7 new tools. First, a tool for the  Fundraising / Grant writing section.

  • Publiconn – Social network for organisations which are users of public or private donor funding and those organisations that provide funding.

Two platforms at the intersection of knowledge discovery tools and science outreach.

  • LiteracyTool – Educational web-platform helping with the discovery, understanding, and exploration of your scientific topics of interest.
  • We Share Science – A place to share, search, organize, and connect research videos across research disciplines.

Two data-focused platforms with social network integration.

  • Delve Health – Comprehensive source of real-time intelligence focused on life science research industry.
  • Datazar – Research collaboration platform where you can easily explore, use and share data.

A platform for literature discovery and reading. With a strong social component.

  • Biohunter – Portal with literature search, data statistics, reading, sorting, storing, field expert identification and journal finder.

And a new kind of collaborative article visualization tool.

  • PaperHive – Simplifying research communication and introducing new ways of collaboration through in-document discussions.

Keep an eye on your lab with TetraScience

tetrascience-normalised-logoIt feels very cliché to say we live in a connected world. But… it’s true isn’t it? We hold our beloved smartphones all day long. Some wear bracelets that track our physical activity. Objects in our homes are connected, allowing us to remotely control the air conditioning systems, lights, and windows blinds. This constant flow of data is supposed to make our lives more efficient, or help us gain special insights on our health. The technology gives us a probably unprecedented feeling of control, and data driven lifestyle is getting traction amongst the general public (us scientists included). But could we say as much for what we do in our laboratories?

Surprisingly, our lab instruments are commonly left alone without any supervision, hoping they will function “as normal” throughout their lifetimes. But of course that is wishful thinking. Most laboratories are like any other buildings. Temperature changes, humidity changes, vibrations comes and go. People turn off equipment by mistake, or turn a knob in a direction or the other. All of it can happen without the experimentalist even noticing.

In these circumstances, it is difficult to truly understand in which environmental conditions experiments are performed. Reproducibility can suffer from this lack of control. When scientists report in protocols experiments at room temperature, what does that truly mean? The “room temperature” in the un-airconditioned laboratory in southern France (Montpellier) I spent my PhD years in was certainly different than the one in my current Northern European research institute.

TetraScience is a company amongst a few others thinking of bringing a new layer of information to modern experimentation. Powered by cloud based software, TetraScience collects and stores data from scientific instruments so that you know what conditions your lab is running in. For instance, TetraScience will stream data from freezers and incubators directly to your mobile device indicating vital parameters such as temperature, humidity CO2 levels, and will notify you when something goes wrong.

TetraScience helps you get concrete idea of how their technology can help researchers through a few case studies. For instance, a happy TetraScience user has been Mathieu Gonidec, a chemist in the Whiteside’s Lab at the Harvard Department of Chemistry.

 “When running experiments, especially those stretching over long periods of time, an error can derail your timeline. Even worse, you are often unsure of what exactly went wrong”, Mathieu says.


In one instance, Mathieu was running a series of experiments where something seemed to not be right. What he discovered from looking at the historical temperature log was that the temperature was fluctuating in swings of 20-30 degrees from the set temperature, causing the experiment to fail.


TetraScience allowed Mathieu to identify the issue, resolve the problem immediately, and move onto the next step of his research.

Here’s another exemple. Jon Barnes is a synthetic chemist in the Johnson Research Group at the MIT Department of Chemistry also told his TetraScience story.

He and his lab seeks to develop new methodologies for the construction and modification of complex material libraries. For years, Jon had been frustrated by the lack of control over simple reaction parameters including temperature monitoring, the ability to turn off a hot plate, as well as to activate a syringe pump from a remote location. Day-to-day experiments often required constant in-person monitoring, which was both inefficient and frustrating.


TetraScience’s real-time monitoring data has granted Jon’s Industry lab peace of mind to start experiments at the end of the day, knowing that they will be immediately alerted if anything goes wrong so they can come back to the lab and take corrective action.

If anyone had tried their services, I would love to hear about your experience. Feel free to comment below!

Nine more digital tool added ot the list

Time for a quick update of the list of digital tools for researchers. A couple tools have been deleted, since they are no longer online. But many more are added. Enjoy!

Data management related tools in the broad sense of the term

  • Dat Data – Open source, decentralized data tool for distributing datasets small and large.
  • Riffyn – Cloud software for visual, collaborative, reproducible innovation.
  • Castor EDC – User friendly and affordable online data collection for medical research.
  • PCR Drive – Free platform that supports researchers in all their PCR-related processes.
  • Ovation – Simplifies your scientific life from sample tracking for startup labs to data management.
  • ELabJournal – GLP-compliant Electronic Lab Notebook and lab management tool.

A collaborative writing tool.

And a couple outreach platforms.

  • Speakezee – Bringing speakers and audiences together.
  • Science Simplified –  A science communication portal aiming to aggregate all academic public releases and serve as a direct communication channel with the general public.

Digital science industry, who are you?

Looking at thquestion-marke digital science industry develop and mature over the past few years has been truly fascinating. There is tremendous excitement from entrepreneurs about the enormous transformative potential of translating new web technologies to the scientific research world. And there are also many frustrations and challenges that come with such major changes in the research and innovation ecosystems.

Although this website and others try to capture these changes and trends, my feeling is that there is yet a clear picture of what the digital science industry looks like. What type of organizations is this emerging community formed of? How well are they doing? How do its actors see the future? Is this even a community? And how can Connected Researchers and other alike can help?

With the help of LabWorm.com, I have created a short survey that aims to fill that gap. Better data about the digital science industry will help the entrepreneur get a better sense of this emerging world-community. It will also make it possible for funders and policy makers to better support the digital science industry. Feel free to fill it in if you define yourself as a scientific tool developer.

Survey — https://thomascrouzier.typeform.com/to/jMMfil —

All results will be anonymized and published on this blog  and LabWorm blogs.