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.

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.

Community-driven discovery of scientific tools with LabWorm

Labworm_logoThere is now a vast ecosystem of digital resources for researchers at our disposal. Digital tools for researchers, science blogs, and databases are a few examples of how the digital revolution can help researchers be more efficient on a daily basis. With this wealth of resources, it is can be easy for researchers to get lost and miss out on important trends. For instance, which blog can help me understand a problem I have been pondering about for days, or what tool can make me write papers with my colleagues across the globe?

Sorting out the the digital resources for researchers is of course not an easy task. Here at Connected Researchers, we manually curate a list of tools, selecting only those specifically designed with researchers in mind. Another approach is to crowdsource this effort, relying on a community to both find and sort interesting resources. Reddit and others have proven the power of such an approach.

Tool Profile Page on LabwormLabWorm is a platform to discover and share digital resources for researchers. The platform is based around a community of tool users (researchers) and the tool developers. Each tool or
resource has it own profile page, with a short description and links to the website and other related resources. There is also a space for discussion, where you can give feedback about your experience or ask questions to other users and the tool developers. LabWorm allows you to up-vote those you like, create collections that you can share with your colleagues, and discuss the tools directly on the site.

There are several ways you will discover new tools on LabWorm.

  1. Every week, LabWorm highlights 5 top voted tools, helping you discover a new tools that your colleagues find useful.
  2.  Similar tools are indicated on tool profile pages. For instance at the bottom of Authorea’s profile page (a collaborative writing platform), two other tools appear. Overleaf, one of Authorea’s direct competitors, and Paperpile, the reference manager for google docs.
  3. Personalized recommendations. Based on the tools in your collection and on your upvotes, LabWorm finds other tools you might be interested in.
  4. Browse by categories and use the search bar. LabWorm sorts the tools by categories and associates tags to each tool, which allows you to search by keywords.
  5. Browse the collections of others. Other LabWorm users have collected their favorite tool and are sharing their collection with you.

Labworm_Screeenshot_1

LabWorm’s social-orientated features and crowdsourcing approach has the potential to quickly curate a large number of researchers’ favorite tools. It could come as a great complement to sites and blogs such as Connected Researchers, which are focused on raising awareness around digital tools for researchers by listing them and placing them in the context of the every day life of a researcher.

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

labfolder_logo

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.