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

The Outsider’s View of the Lab

Steve McCoy from TetraScience talks about how his idealized high-tech perception of research was confronted by the low-tech reality he witnessed when entering the life sciences industry.

In 2016, millions of people worldwide invited a complete stranger into their homes, and immediately she made an impact for the better. Amazon recently announced that its Echo and Echo Dot – devices powered by the voice-controlled system Alexa, were best sellers for the retail giant over the recent holiday period; so popular, in fact, that the devices were on back order into 2017 .

If this isn’t a sign that connectivity is the new rising star of tech, I’m not sure what is. With smart tech continuing to expand rapidly, people now expect their home devices, gadgets, even their cars to sync seamlessly and with little effort. “Internet-of-Things”, “Smart Home”, “Wearables”, “Smart Cities”, and “Connected Car” are now everyday terms used to describe the collective concept of connected devices, and although still a relatively new phenomenon, connectivity has already made quite the impact.

And the positive implications of the adoption of this technology speaks for itself. Tech Times reported that employees using wearables reported an 8.5% increase in productivity. In fact, the US Department of Transportation is converting Columbus, Ohio into a smart city; complete with self-driving electric shuttles, high-speed WiFi stations, and better transportation to areas within the city. As this new technology is embraced in the gym, the city, and our automobiles, we should expect to see similar improvements made in our work environments as well, right?

Having entered the life sciences industry about 8 months ago, I expected smart technology to already have widespread adoption. Prior to joining TetraScience, my experience in labs was primarily limited to Hollywood depictions. While scientists are not currently extracting dinosaur DNA from mosquitoes trapped in petrified amber (we’re not far off), it is still hard to think of R&D as anything but the embodiment of innovation. 60 Minutes, VICE, and Business Insider continually delivers news on a weekly, if not daily basis, about all of the cool discoveries and processes R&D scientists are unearthing. Naturally, one would expect the instruments and technology employed in research to be a reflection of this cutting-edge image .

But, that assumption was only half correct. Scientific instruments are some of the coolest instruments I’ve seen, with capabilities that are simply mind-boggling for non-scientists. The technology that powers them, on the other hand, leaves plenty to be questioned. Freezers and refrigerators recording temperatures via circle paper graphs must be manually collected and physically filed (yet Kristen Bell and Dax Shepard have a fridge that can order food and provide a real-time view of their shelves).  Analytical instruments that can cost upwards of $100,000 still  require users download information onto a thumb drive before walking over to their work station for uploading onto a different computer. With thumb-drives becoming a tech relic, getting data from these instruments should not be so complicated.

How can an industry that has driven innovation in so many different arenas be content with such antiquated tech practices? Many I’ve spoken with in R&D cite the hundreds of different hardware manufacturers as the root cause, but with plenty of smart tech brands readily available, this issue should be easily remedied. Pen-and-paper methods should remain an option, but not the norm, but for many R&D labs and scientists, the opposite holds true, and for the most part, it’s become accepted.

But don’t be mistaken: as with connected devices in our daily lives, there are implications to life in the lab without connectivity. Deloitte’s annual study on pharmaceutical innovation showed that profits on cash investment for big pharma is at an all-time low (3.7%), due to shrinking profits and plateaued development costs. A shrinking ROI means that there’s less budget to invest in the latest instruments, additional staff, and/or new investigations & projects.

What did Deloitte cite as one of its three key findings to reduce R&D costs? Lifting the burden of data complexity. Downsizing the amount of time spent on low-value tasks, such as moving data from an instrument to an ELN (what we call “data-jockeying”), can help R&D personnel focus on the more technical complications of data management. An apathetic approach to getting more from technology providers, however, won’t let this initiative happen anytime soon.

Thankfully, there’s been a growing number companies addressing the need for connectivity in the lab. A few of those that come to mind are Benchling, LabGuru, and of course, TetraScience. To accelerate the availability and capabilities of technologies that those companies offer, scientists must demand the industry behemoths improve their own offerings. Change won’t come overnight, and it certainly won’t be without its faults (just ask Alexa), but it’s time that R&D labs catch-up with their public perception.

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.

Five new tools added to the toolbox!

Ftoolbox-152140_640ive tools today added to the list today to hep researchers in their every day tasks. Find the complete list on the online tools for researchers page. I’ve also added a graph digitizer (dcsDigitiser) to the list you can find in this blog post.

  • Lab SuitInventory Management, orders Management, materials Trade-In, price Comparison.

So what’s “trade-in”? Well, it is simply opening up your lab inventory to other researchers. The more give away, the more you can ask others in return. A potentially great way to formalize the reagent exchange emailing list that most departments have.

  • Journal of Brief Ideas – Provides a place for short ideas to be described – in 200 words or less -, archived, searchable and citable.

This is based of the concept that ideas are common resource, and that it is only the way the idea is acted upon that should be attributed to group or individuals. Also check out the RIO journal that offers researchers to publish their research proposals.

  • SciFeed – Uses various data sources and natural language processing to identify important new scientific advances.

Probably a good way to keep on top of major scientific advances in all fields. This however won’t analyze your interest to suggest recent articles in your field.

  • LifeScience.net – Online platform for professional networking and sharing of knowledge in life sciences.

There, you will find a number of announcements related to the life sciences. Jobs, events, news, publications and protocols. Haven’t tried it myself.

  • F1000 workspace – A workspace for scientists to collect, write and discuss scientific literature.

The latest project from the F100 publishing platform. Check out the short video below.

F1000 – Writing Tools For Scientists from F1000 on Vimeo.

Explain, enrich, and disseminate your research with Kudos

Kudos, is a UK-based company launched in 2013 that helps researchers and research institutions disseminate published research and increase its impact. Authors of published article can create a Kudos profile for their papers, providing an easy-to-understand summary and links to related documents.

So here is my first personal experience with Kudos. I took the last piece of work that I published this year. Kudos finds your published articles very easily, either after entering their DOIs or by connecting Kudos to your ORCID account.

Kudos then guides you through a series of steps. First, you need to choose a short title, free of technical terms. Ideally, the title should give the reader a mental image of what the work is about. The original title of my article was reasonably short : Covalently-crosslinked mucin biopolymer hydrogels for sustained drug delivery. But I made it a bit shorter and a bit more popular-science sounding: Medical device made of mucus delivers drugs.

Screen Shot 2015-09-03 at 11.22.37 AM

Paper profile page where the authors directly edits the short summary and links related documents

Then, you are prompted to write a little blurb about what the article deals with. Try to describe your work like you were talking to your friends that have no clue about scientific research. I’m not sure what it is worth, but here’s mine:

Drugs are often much more effective when delivered from inside the body,  slowly diffusing out from an implant. For instance, hip implants can release antibiotics to prevent infections, or gels loaded with anticancer drugs can be injected to kill tumors more efficiently. But designing materials that slowly release drugs can be challenging. A solution is to look towards nature. Polymers found in animals and plants are have plenty of interesting functionalities and are often well accepted by the body when implanted. Mucins are polymers that composes our mucus, the slimy gel that covers our eyes, nose, lungs, stomach, intestines, and the female reproductive tract. The mucus gel protects us from harmful particles, bacteria and viruses, by binding to them before they have a chance to enter the body. This sticky property is what we exploited here. We built a gel made of sticky mucins, loaded drugs inside the gel and measured their release over time. We saw that thanks to mucins’ stickiness, two very different drugs slowly released from the gel. For instance, antibiotics where release so slowly from the mucin gels that bacteria could not grow anywhere near the gel for over a month!

But you’re not done yet. What most people care about is not the how, it is the why. Why should I care? Kudos asks you to write a few lines about the significance of the work. Here’s my significance paragraph:

Although mucins are highly functional molecules and abundant in nature, they have not been used in technological applications. This article describes for the first time the assembly of mucins into a stiff hydrogel, and shows that their ability to bind certain molecules can be exploited for biomedical applications. This work should lead to other mucin-based biomaterials.

Finally, Kudos suggests that you provide a more personal view of the publication. This time, you are not speaking for all the authors, but just for yourself. I thought I would give my feeling about the paper and explain why I am excited and somewhat attached to it:

This is an exciting piece of work that I think could lead to many others. Of course, many challenges lie ahead before mucins can be used in biomedical applications. But as we move forward, we are learning about mucins’ fascinating properties and how to assemble mucins into functional materials that might have applications that we cannot foresee today.

OnScreen Shot 2015-09-03 at 12.05.58 PMce you’ve filled all of that in, you are invited to add links to any related documents. This is where you can link to an open access version of the paper in your self-archiving or institutional repository, add links towards related news articles or presentation slides that you might have shared on Slideshare. I linked a version of the article I stored on Zenodo and an infographic I’ve had made to explain the research through images.

The paper’s Kudos profile page is now complete! It will appear very similarly to the way it is displayed when you edited it. The way the summary is displayed could be improved a bit by making the screen a bit less dens in information, and by focusing a bit more on the text (which could use a slightly bigger font). I would also love to be able to add an image or two to illustrate the summary. But it still does the job!

Now that you’ve filled in all the requirements, it is time to share your Kudos paper profile with the world. You can link your social media accounts with Kudos, so that they help you spread the word. Or, you can get a short link and tweet it, mail it, or post it wherever you like.

Screen Shot 2015-09-03 at 12.07.09 PM

Disseminate your work through social media, or any other way by using a short url to your Kudos paper summary page.

Once it’s out, you can follow the impact of your Kudos paper profile on your Kudos dashboard. Through a collaboration with the Web of Science database and Altmetrics that tracks social media sharing of scientific articles, Kudos tell you how well your article is doing.

I’ve shared my Kudos profile on twitter and included a link in a post on LinkedIn and on Facebook and got these stats after a couple days:

Screen Shot 2015-09-08 at 11.13.55 AM

Hard to say what the impact on citations mights be in the long run, but I am guessing this kind of thing cannot hurt. On their website, Kudos claims that “in a pilot version of Kudos during 2013, researchers using the Kudos sharing tools saw an average increase in downloads of their publications of 19% compared to a control group”. Whatever the final outcome, this is a great platform to encourage researchers to start communicating about their research to a larger audience. It is easy to use, not too time consuming, and very importantly, Kudos rewards the researchers almost immediately for their efforts by providing metrics of how the Kudos profile and the article are doing.

6 digital tools for researchers added to the list.

Back after a short break with a series of new tools to the list of digital tools for researchers.

TScreen Shot 2015-08-28 at 5.26.50 PMhis is part of Elsevier’s SciVal platform, providing research institution and universities with research intelligence, including on their own research production. This service is only available through a subscription.

This service provide up to date news about research throughout the world, and alerts about funding opportunities. Also available through a subscription.

  • Screen Shot 2015-08-28 at 5.28.14 PMProfology – A professional community created exclusively for higher education faculty, staff and administrators.

A free social network for the non-students of higher eduction.The idea is to provide the staff with a more private space than what you might get on Facebook. Professor can share tip and trick about teaching or management of research groups without the risk of students bumping into it.

  • Kudos – Helps researchers explain, enrich and share their publications for greater research impact.

Screen Shot 2015-08-28 at 5.25.06 PMThis is good one. I will try to post a more extended post on Kudos soon. It provides authors with a space to explain their work in a way everyone can understand and link other ressources to the published article. A great way to increase the visibility of your published work.

  • Citavi – Reference management, knowledge organization, and task planning solution.

This Switzerland-based company offers a complete solution for your reference management. I have not tried it myself, but would love to hear from its users. Windows only for now.

  • InSIlico DB – Genomics made possible for biologists without programming.

This online platform seems like a great for those needing to use bio-informatic tools. It combines on the same platform an easy access to genome database with analysis tools. Have a look at this video from more info.



From paper discovery to research group site with Labii

Screen Shot 2015-07-02 at 10.35.37 AMLabii is a young startup developing a series of interesting tools for researchers. They have already released three applications:

  1. A Research Group app to easily create a web page for academic research groups.
  2. A Profile app that provides a online CV page  and manage the user’s activity on Labii.
  3. Reference Manager app to find, collect and rate papers.

An electronic lab notebook is also coming our way int he near future.

Webpage for research groups.
Having an online presence is essential for research groups. It attracts students and postdocs, helps create new academic and industrial partnerships, and can inform the general public and the media about the group’s research activities. But building a new site from scratch can cost thousands of dollars. And not all young independent researcher can afford it at the beginning of their career, when they actually need it most.

Labii offers a free and immediate online presence by building a groupe site. The site can contain a short description of the group’s research interests, the latest news from the group, contact information and picture of the principal investigator, a summary of the research projects, a list of group members, and a list of publications (view an example of a Group site). The result are a simple but good looking websites that provide all the basic information a research groups might want to communicate.

Star rating and comments.
Screen Shot 2015-07-02 at 10.30.54 AMThe reference manager combines traditional paper discovery and personal library tools, with the ability to comment and rate papers. Paper references are accessed through the Pubmed database search or by subscribing to specific journals. Labii then displays the paper’s metadata including an altmetrics score that tracks the mention of the paper on social media, as well as more traditional metrics such as number of views on the site, comments, and citation.

Each paper can also be commented or discussed on anonymously or not. The commentsScreen Shot 2015-07-02 at 10.30.43 AM are ment for short notes or questions about the work. The discussion allows authors and readers to go beyond the results presented in the paper and link to new references or results. This is also the place to brainstorm about new ideas, point out mistakes or possible improvements.

A profile page for researchers.
The profile page provides a public CV for researchers and identifies users when commenting on papers. Similar to other profile page such as ORCID and ResearchID, researchers can display their education background, and their professional accomplishments.

Final word.
The idea to combine tools targeted at different stage of the research cycle within a centralized platform seem like a great idea. Researchers have much to gain from a single platform can help them search articles, record experiments, peer-review papers, and communicate on their findings (through profile pages, but also by publishing research results). This would prevent them from going back and forth between different tools, with different standards. The road to such a unified system is still long, but Labii is courageously taking on many of these aspects at once. If successful this could result in one of the first unified digital all-inclusive platforms for researchers.

4 more digital tools for researchers!

matt-icons_folder-add-1Here is another update of the list of digital tools for researchers with three new entries. I haven’t been posting as much as I would have liked to these past couple of months. My recent move to Stockholm (I am starting a new posting at the Royal Institute of Technology, KTH) has been taking most of my time. Thank you for all of you commenting and pointing out new tools!

  • GitLab – A git repository management, code reviews, issue tracking and wiki’s all in one platform.
  • Innocentive – Helps clients to engage a world of creative and diverse on-demand talent to rapidly generate novel ideas and solve important problems.
  • BiomedUSA – Global open access hub for sharing and licensing of Biological Research Materials and related technologies.
  • Data Elixir – A weekly collection of the best data science news, resources, and inspirations from around the web.

A new open access infographic journal: Draw Science


Science outreach benefits nearly everyone. The general public is better informed, has a better idea of how their taxes are being spent, and in the process trust the scientific enterprise a bit more. Politicians and mZVQS-23administrators can decide on more rational policies. And researchers get recognized for their work and benefit from a science-friendly society through more generous funding. More and more is being done to encourage researcher to reach out to the general public. But the main mean of communication for researchers remains the research article. These are long, technical, text-heavy documents that are hard to understand for the layperson. Wouldn’t it be nice if with a single article, researchers could communicate with both their peers and the general public?

Draw Science is making research articles accessible to all by transforming them into infographics. The information is summarized and visualized into easy-to-undertand schematics and images. The important message sticks, while distracting details are brushed away.

Based on the success of the Draw Science website, Viputheshwar Sitaraman, founder of Draw Science now wants to formalize this by creating a Draw Science open access journal. Submissions of articles will be reviewed and the selected articles transformed into infographics. Each infographic will be freely accessible and individually identified by a DOI. Viputheshwar has started a funding campaign on experiments.com to get this project started. The goal of $1,100 is modest but should get this innovative idea off the ground and allow it to function for a year.


Communicating science to the public – ScienceGist closes, many others still in business!

ScienceGist_small_logoScienceGist, a platforming offering lay summaries of research articles, just announced they are going online after 2 good years of loyal service. This comes as a bit of a sad news, especially at a time where the ability of researchers to communicate with the general public is increasingly important.  But this is also an opportunity to shine some light on a few other similar initiatives:

  1. UsefulScience – Summaries of the latest science useful in life
  2. SciWorthy – A science news site for the everyday person to better understand science
  3. GMTRY – Transforms science into art.
  4. Publiscize – Empowering scientists to free science and make their research available to everyone
  5. AcaWiki – Summarizing academia and quasi-academia, one document at a time

Thanks to @ScienceGist and @benmarwick for the links I didn’t know about.