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Electronic lab notebooks and the future of science discussed at Labfolder workshop


I was fortunate to attend a Labfolder workshop on the 2nd and 3rd of June 2016 in Berlin (Germany). This was the opportunity to discuss user experiences of Labfolder’s electronic lab notebook (eLN), but also to talk more generally about digital science tools and their integration the researcher’s workflow. I thought I would share what I’ve learned during that session.

The session first started with a presentation of the smartLAB initiative from the Institute of Technical Chemistry at Leibniz University Hannover (Germany). There, a research group is developing the lab of the future, both on the hardware and software integration side. They have a few fascinating videos that shows very concretely what a fully digitalized laboratory could soon look like.

A prototype of their concept developed with several partners including Labfolder has already been presented to the public earlier this year. Dr. Patrick Lindner represented the project, and mostly talked about their smartLAB’s efforts to connect laboratory instruments to the internet and about their collaboration with Labfolder to directly feed the data back to an eLN.

Then, Dr. Alexander Grossman discussed about the ScienceOpen platform that he launched in 2014. ScienceOpen now aggregates of over 15 million articles, with the possibility of post-publication peer review (commenting) and articles rating. But ScienceOpen is also set up as a publishing platform. Researchers can prepare manuscripts directly on the platform, then release their draft as a publication when they are ready. The article then relies on post-publication peer review for its quality control, receiving only an editorial check before publication. Perhaps the future of scientific publication?

Prof. Ulrich Dirnagl, director of the department of Experimental Neurology at the Charité medical university in Berlin (Germany), gave an impressive talk about their efforts to bring data management into the 21st century. They realized that electronic lab notebooks are essential to improve sustainability of data, its findability, and the reproducibility of experiments. He pointed out to an article he published at the beginning of 2016 that constitutes a handbook for introducing eLN in academic life sciences laboratories. He starts the article with this striking image of two lab notebook entries looking very similar despite over a hundred years of history separating them. His message: surely we can do better today.

Image from Dirnagl, U. & Przesdzing, I. A pocket guide to electronic laboratory notebooks in the academic life sciences. F1000Res. 5, 2 (2016).

Image from Dirnagl, U. & Przesdzing, I. A pocket guide to electronic laboratory notebooks in the academic life sciences. F1000Res. 5, 2 (2016).

Prof. Dirnagl also explained how he led efforts to equip his department with an ISO 9001- certified quality management system. First, this means they had to think about a system to manage the quality of the work conducted in the department (which is already beyond what any lab I have worked in has ever done). Then, they had to made sure this system would meet the type of strict requirements ISO norms usually entail. A courageous initiative since ISO norms are nearly never found in academic laboratories, which are more accustomed to improvisation than standardization. Although it required habit changes, Prof Dirnagl explained the personnel was overall enthusiastic about the changes and that the laboratory is now certified. Prof. Dirnagl is now assessing the impact of the certification on the quality of research and is reflecting about alternative quality-control standards that could be more adapted to academic setting.

Of course industrials routinely adopt such standards because of strict regulations and the strong marketing impact ISO-certifications can have. Dr. Sam Moré is director of a nanotechnology company called DendroPharm that develops nano-drug delivery vehicles for veterinary applications. Dr. Moré explained that their quality management system is also certified ISO 9001 and described how the use of a eLN was essential in that process.

Finally, on day 2, Joram Schimmeyer a PhD student in the Max Planck Institute of Molecular Plant Physiology in Potsdam (Germany) presented his digital research workflow. He explained how nearly all of his work is now in digital form and how an eLN fits perfectly in that workflow.

In addition to these amazing talks, the workshop was an opportunity to talk about the future of the electronic lab notebook and how they fit in the future of science as a whole. These were interesting discussions, that I leave for another post.

BioBright brings the internet of things to the lab.

Biobright_logoA digital revolution is transforming scientific research into a more open, more interconnected, more global, and more data-driven endeavor. Many of these changes are driven by new digital infrastructure.

But science is also done in the laboratory and in the field. Experimentalist need to prepare solutions, calibrate complex instruments, and make measurements on samples. This more down to earth aspect of research has gotten a bit less attention from open science and digital science enthusiasts. However new approaches and new tools may improve the way we do research in the lab. A handful of digital science companies are already thinking how digitalization and connection to the internet can improve the way we use scientific instruments. For instance Transcriptic and Emerald Cloud Lab have installed armies of robots in their Silicone Valley warehouse (or at least that is how I imagine it) that are awaiting your orders to perform experiments. The results are then delivered directly to your computer screen.

BioBright, a startup out of MIT and Harvard University , wants to connect our lab instruments. The idea is that connecting sensors to your instruments, even the most simple one, would give you more control and a better understanding of the exact conditions in which the experiment was done.

weather-1216041_640Practically, BioBright is working on a collection of sensors and software solutions that can be associated to the most common lab instruments. These extra pieces of data could provide the experimentalist with precious details about the environment in which the experiment was done, making it easier to troubleshoot or reproduce the experiment. BioBright has already mentioned connecting thermometers, but other sensors such as hydrometers, motion sensors, and light sensors could also be useful. Eventually, these measurements could be automatically associated to the data generated by the instrument, then transmitted and archived in electronic lab notebook.

BioBright is one of the first to bring the internet of things (or internet of instruments as mentioned by this Techcrunch article) to the research laboratories. It has taken years for web 2.0 technologies to reach researchers. But perhaps BioBright and others related initiatives such as TetraScience, are early signs that innovative connected scientific instruments will be developed alongside the recent and very trendy connected home technologies (and not 10 years later).

New Impactstory: fresh and free!

Impactstory-logo-2014Impactstory tracks the online impact of your research. It looks through news outlets, social media mentions, and more to quantify the reach of your research output. Impactstory is one of the first startup founded around the idea that a new set of metrics is needed to properly evaluate scientific research and researchers. The digitalization of research and scholarly communication is an amazing opportunity to harness very large quantities of quantifiable data, which can give completely new insights in the impact of research. Many now talk about altmetrics, a term originally coined on Twitter by Jason Priem, co-founder of Impactstory. These new metrics are still young and will need a few rounds of trial and error to find out what information and what representation of the information are the most meaningful. But regardless, altmetrics are bound to become essential for the future of research evaluation.

mentionsThe new profile page has a very fresh and clear look. Login is now only through ORCID, the unique identifier system for researchers. Then within seconds, Impactstory recovers your published articles and generates an overview of your mentions, which give you numbers on your online reach. But Impactstory tries to give perspective to these number though what they call achievements. These are badges focused on

  • the buzz your research is creating (volume of online discussion),
  • the engagement your research is getting, which looks at the details of who is mentioning you, and on what platform.
  • and your research’s openness, which look at how easy it is for readers to access your work.

For many of these badges, Impactstory also tell you how well you are doing compared to Softwareother researchers. One particularly interesting badge is about software reuse. There, Impactstory has integrated a tool that they recently released called Depsy. Depsy is specialized in evaluating the impact of research software, going beyond formal citations to understand how research software are being reused and to give proper credit to its contributors. This will deserve a post of its own in the future.

Hopefully, these sets of metrics and others alike, will become a standard part of your performance reviews, grant applications, and tenure packages in a very near future. You can already share your profile by directly pointing to your public Impact Story url. But new features will come shortly to make it easier to share and showcase the story of your online impact.

Visualizing DNA sequences made easier with new add-on

genomecompiler_logoMany online tools help researchers analyze and manipulate genetic data. Usually, the DNA sequence is first looked up in specialized databases, and copy-pasted into various forms. These tools have been incredibly useful to researchers, but are not visual, not collaborative, and are often very specialized. A number of online platforms now bring together sets of bioinformatic tools for genomic analysis and design. These cloud-based services make it easy to save and share data and results with collaborators. They are also directly connected to large public databases, which makes it easier to import the data you would like to work on. A few are already listed on the list of digital tools for researchers.

  • 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.
  • InSIlico DB – Genomics made possible for biologists without programming.
  • And many others are not listed here.

These services also made the visual experience more pleasant and allows you to directly interact with the sequences you are working with.  This new way to handle and share genomic data is now taken a step further by GenomeCompiler, which has recently launched a new service called Plasmid Viewer. This free add-on can be embedded into websites that have DNA sequences repositories. This is done rather easily by pointing to a GenBank file url. The viewer then interprets the file and displays the DNA sequences as interactive sequence or circular representations along with annotations.

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Screenshot from genomecompiler.com displaying their new plasmid viewer add-on

This new tool should help researchers share their genomic data in a more visual and meaningful way, for instance on group websites or scientific blogs. One example of how it can be put into use is this group’s website that has a list of vectors they use for cloning and use the plugin for their visualization. You will also find a demo on the GenomicCompiler.

Going beyond impact factor to evaluate researchers with Profeza

ProfezaFor many reasons, journal impact factor and number of publications are not good metrics to assess the quality of a researcher’s work. But regardless of their increasingly bad reputations, these metrics are nearly invariably used to take decisions about recruitments of researchers, their promotions, and funding their projects. The obvious reason why nothing has changed over the years is because there are no other easy way to judge the quality of a researcher and his or her work.

We ask a lot of researchers. They must be great at scientific reasoning and have bright insights but also be able to properly communicate with their teams, with the scientific community, with the general public, and with industrial partners. They also need to be able to network and work within teams, to manage projects and people, to teach, and to write skillfully in a language that is often not their own. It is easy to see that we would need a multitude of alternative metrics to properly evaluate the various aspects of the day-to-day work of researchers. 

Profeza is a young startup that would like to provide decision makers a better overview of the work of researchers. It has launched a social journal that allows researchers to showcase the divers aspects of their work by sharing the rational of experimental design, the failed hypotheses, as well as raw data, repeat data, and supporting data that would otherwise often go unpublished. For Profeza, each scientific article is only the tip of the iceberg, standing on a immense amount of work. 

Profeza’s interface is simple and clear. First, find the publications you authored through Profeza’s search engine. Profeza’s is currently using the Pubmed database and is thus better optimized for researchers in the biomedical fields. Then in three steps you are prompted to add information to the publication:

1. Select the publication you wish to add information to.

Share contributions2. Describe your contribution to the paper and invite other authors that may not be in the author list but should get recognition for their involvement in the work.

What contribution

3. Add information. You can add text and files containing the details about the rational of design, failed hypotheses, raw data, repeat and supporting data. This is a great way to help others in your field by tell them about your failures or negative results.

Additional data

The end result is a personalized page for each article containing the additional data and information. The page gives a better picture of the work that went into the publication and provides an insight in the short term impact of the articles by displaying altmetric data. 

I think Profeza is addressing a real problem head-on. The success will of course depend on the willingness of researchers to spend time formatting and entering the information and datasets. But if institutions are willing to play along, then the incentives would be in place and a more adapted evaluation system could emerge. These are still the early days. Profeza was founded in 2014 and expects to roll out new functionalities in the near future.

Also check out this well-crafted video from Profeza which gives a nice background on journal impact factors and the problems associated with them.

SJfinder gets a serious update

SJFinder logoA group of scientists and technologists from Stanford University (US) and KU Leuven (Belgium) launched SJFinder in 2013 to help researchers find the right journal to publish in based on the title and abstract of their manuscript. Since then a number of new functionalities have been added to the site. The idea is to offer a collection of tools to researchers to give them more control over their networking and communication. 

Rate Journal SJFinder

Rate journals on SJFinder

Beyond the journal suggestions, SJFinder now also allow you to rate journals based on their reading and submission experiences. In an ideal world, submission would be chosen not on impact factor, but 1) on the traditional readership of the journal (if any) and 2) on the quality of the service provided by the publisher (i.e smoothness of peer review process, delay from submission to online availability, metrics on article, promotion of article).

SJFinder also helps you discover the literature, like other tools out there. In this case the simplicity of the user interface is especially appealing. Simply click on the fields that most interest you, and SJFinder will generate a list of the latest papers in that field. You can also subscribe by journal, but I personally think there something nice about exploring the literature by field and not by journal. Perhaps it is because it makes me less journal-biased and make it more likely to stumble upon interesting works and concepts.

map SJFinder

Find labs by exploring a map on SJFinder

To help you find new collaborations and showcase your work, SJFinder rolled out two other functionalities. First, an interactive map helps you find research labs anywhere in the world. You can brows the labs by research fields, location, or by keyword, and explore the map. You can also easily add your own labs to the directory. The benefit of having a world-wide database of lab displayed on a map is pretty clear to me. I would use it to find new local collaborations. Sometime a hallway is enough to separate groups that would otherwise collaborate wonderfully. Or to find laboratories that I could easily go visit while at a conference.

And second, SJFinder launched a drag-and-drop website builder to let you build a website for your lab. This will makes it possible for the many researchers with limited resources of time and capital to create a website and showcase their work. It might sound almost old fashioned, but in my mind a website is a must for any research group. This, along with other similar tools, are great way to get started at building your online presence.

sciNote Kickstarts their open source electronic lab notebook

logo_sciNote_final-300x54An open source electronic lab notebook is launching a Kickstarter campaign to officially launch its beta version. sciNote, stems from BioSistemika,  a five year old Bio-IT company from Slovenia, which develops digital tools and on-demand software for research in the life science fields. For instance, their tools help research manage qPCR experiment workflows or offer an interesting way to help pipetting in multi-well plates. But sciNote is applicable to most scientific fields of research. It differs in several ways from its main competitors such as LabGuru, Labfolder, LabArchive and many more.

  • Open source. The software behind sciNote will be released under the open source Mozilla Public Licence (MPL). The entire source code will be available on GitHub upon the release in the early 2016.
  • Modular. sciNote will develop there own additional functionalities and will open the code to anyone to develop their own. These plugins will adapt the software to the specific needs of each laboratory.
  • Experiment workflows. With workflows, one can link different phase of a project (i.e. Sample preparation –> DNA extraction –> Molecular analysis). This connects the data obtained during various phase of a project or experiment and puts the data in its broader context. The logical progression of the lab notebook entries is clear, even years after the person doing the experiments  has left the laboratory.
  • Free. Well, most other electronic lab notebook are free to access. But sciNote does offer a larger range of functionalities for free. Complimentary space will be included for free and users will be able to get more free space by inviting other people to sciNote (smilar to Dropxbox). However for larger storage, additional space will be available for purchase.

I have not tried sciNote myself. But from their description it seems to come close to what LabGuru (perhaps the most complete electronic lab notebook solution accessible to academic researchers) is offering. Their Kickstarter aims at securing $12,000 to start the beta phase and help pay for server costs. As of today, they are only about $2,000 short.

Report: Science Ecosystem 2.0: how will change occur?

book-933088_640The advent of Open Science and the digital technologies enabling open science is facing researchers with many changes in the way they are doing science, communicating science, and being evaluated. Connected Researcher does its part by helping researchers transition towards a more open and collaborative science by introducing them specialized digital tools.

But the European Commission, led by the commissioner for research, science and innovation Carlos Moedas, has also been very pro-active at looking at how the research and innovation ecosystems are being effected by digital technologies and other changes in organizational and work habits. They have launched major public consultation in the summer of 2014 and have now started to suggest rather ambitious policy actions (such as the launch of a common Cloud for researchers).

I was commissioned a report describing what the future of Science and innovation ecosystem could look like in an Open Science world. The report was commissioned as part of the activities of the Research, Innovation, and Science Policy Experts” (RISE) high level group. The mission of the RISE group is described on the EC’s website as follows.

RISE gives direct strategic support to the European Commissioner for research, innovation, and science and to the European Commission. It focuses on how to best use EU research, innovation, and science policy to address the European growth model and to create the conditions for a different type of growth, a growth that is smart, economically and environmentally sustainable, and socially inclusive for the EU and associated countries within a globalized world.

have a look if you are interested. The report is available on the European data sharing platform Zenodo: https://zenodo.org/record/33044

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.

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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.

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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:

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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.