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!

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).

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.

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.

Cellkulture shut down, but code alive on Github

Screen Shot 2014-08-26 at 2.47.24 PMCellKuture, the digital lab notebook that helps you track and manage cell cultures, shut down 5 months ago. But although the project in not actively being developed, the code lives on, published on the Github repository, free for anyone to use.

Startup turnover is a very natural thing to happen in the new space of Digital Science. Entrepreneurs simply cannot have a perfectly clear vision of what the research ecosystem will look like in a few years. Startups are taking their chances by exploring new markets and testing the reactions of customers to new services. And in this context, it can be hard to gather enough users to really push your startup off the ground, especially when targeting a niche market (like cell culture experts).

A consequence of this high-risk environment, is the sense of responsibility we should expect from these digital science startups. They should think in advance of opt-out options for users changing providers or if the company goes under. This means providing ways to export the data in a reusable format, and in some cases, providing the code so that users can continue to use the platform. CellKuture is doing exactly that by providing a functional software for free with instructions to install and run it. On top of making CellKulture users happy, this move could attract new users, and most importantly inspire other developers to build upon this piece of work.

Graph digitizer comparison – 16 ways to digitize your data (updated)

progress-01Although pdf files are the current standard for the dissemination of scientific knowledge, the format comes with several, well known, drawbacks. An important limitation is the difficulty to re-use the data embedded in graphs and plots. Even with the advent of “enhanced” html versions of articles, data is still most often represented with images, which makes it difficult to extract the raw numbers. A few initiatives from publishers now ask researchers to submit their data along with their manuscript. But for the millions of paper already published, a number of different software solutions can help you digitize the data from plots and graphs.

Digitize your graphs and plots

All the tools presented below follow a similar process to convert bars graphs, scatter plots, and line plots into a series of numbers.

 1. Open a graph

1270668950Depending on the software, the graph can be imported directly from a .pdf file, or will first have te be converted to an image format (jpg, bmp, png, gif…). The image can be obtained through the html version of the paper, or by taking a screenshot of the pdf file (on Mac use command-Shift-4; on Windows use the print screen button or by use the Snipping Tool; on Linux use the Take Screenshot application). When saving your screenshot, be aware of what file format your software accepts.

 2. Set the scale

TWebPlotDigitizerhe software will ask you to define the axis and set the scale. This is how it will define the coordinates of each point. The more precise you are while doing this, the better your results will be. Most software allow for distorted axis (not perfectly perpendicular). And remember to indicate wether the graph is in log scale. (the image to the left taken from WebPlotDigitizer).

 3. Digitize the data points

WebPlotDigitizerYou then need to digitize the points or lines. Depending on the software, this step is going to be more or less automated. Most often, you are asked to, at least approximatively, indicate where the points or lines are located. Some fully manual will ask you to draw over the points or line in order to digitize the data.

 4. Export the data

export-3Finally, copy and export your data into the format that is most convenient to you. Some software include additional acquisition data analysis functionalities. But most often this is done by simply pasting a table of coordinates in your favorite data processing software.

 

Comparative study of graph digitizer softwares

We have put together a comparison table of 16 graph digitizer software. There might be others out there worth mentioning. Please do not hesitate to comment and we will add them to the list.

 plateformcostautomatic detectionfiles supportedpost aquisition analysisyear
Dagra: Digitize graphical dataWindows$49.95yes~ all image formatsno2012
DataThiefWindows, MacOS, Unix$25noJPG, PNG, GIFno2006
dcsDigitiserWindows$423yes~ all image formatsyes2015
DigitizeItWindows, MacOS, Unix$49yes~ all image formatsno2014
EngaugeWindows, MacOS, UnixFreeyes~ all image formatsno2015
g3dataWindowsFreeno~ all image formatsno2011
Get DataWindowsFreeyes~ all image formatsno2013
Graph ClickMacOSFreeyes~ all image formatsno2014
im2graphWindows, LinuxFreeyes~ all image formatsno2015
Graph Data ExtractorWindowsFreenoBMP, JPG, TIF, GIF, and PNGno2011
Image J pluginWindows, MacOS, UnixFreeno~ all image formatsno2014
MATLAB tool (Grabit)Windows, MacOS, UnixFreenoBMP, JPG, TIF, GIF, PNGyes2007
Plot DigitizerWindows, MacOS, UnixFreenoJPG, PNG, GIFno2014
Un-Scan itWindows, MacOS$345yes~ all image formatsyes2014
WebPlotDigitzerWeb basedFreeyes~ all image formats no2014
WinDig Data digitizerWindowsFreenoBMPno1994
xyExtract Graph DigitizerWindows$45noBMPno2011

So what solution is best for you? Well, as often, it depends. For most cases, using the browser-based WebPlotDigitzer will be the most convenient. It handles many types of graphs and plots, while being free. It does not require any installation, and is compatible with all platforms. You might want to consider however that because WebPlotDigitizer is a web-based tool, the current software version number is unknown, which makes it hard to reference the analysis you will have done with precision and can get in the way of reproducibility.

For the more demanding situations, Un-Scan it might help, since comes with the longest list of functionalities. It is also the most expensive solution listed here.

Also, if you are a R user, you will find tutorials online on how R can help you extract data from graphs, and a paper describing a dedicated R package developed by Timothée Poisot.

Please comment and share your experience with these tools! Many thanks to David LeBauer for his insights and comments.

Update (30th of July 2015). I have added to the list im2graph

Outsourcing experiments made easy thanks to Science Exchange

SE_Logo_LargeScience Exchange is an online platform to find the best contract research organization (CRO) to help you in your experiments.

Why Science Exchange?

Science is an increasingly collaborative endeavor. The problems tackled by today’s researchers require a variety of expertise, skills, and scientific equipment. Although large research institutions usually find the necessary collaborations and technical platforms, smaller labs can struggle to find the expertise or instruments they need.

Several online platforms are now trying to connect researchers to their peers and to experts of all sorts to facilitate collaborations (to learn more, go to the Digital Tools for Researchers list). Science Exchange is one of these platforms. Founded in 2011, it connects researchers with research service providers and an impressive selection of over 1000 assays. The service providers range from core facilities of academic institutions to startups and biotech companies.

I need help on an experiment, how does this work?

Simply start by searching the type of service you are looking for. Say I want to analyze a protein sample by Western Blot, but am not equipped in my lab. The search “Western blot” returns over 30 service providers, with various prices, number of positive reviews,  and time to delivery.

ScienceExchange search

A list of providers that offer Western Blot analysis services.

Click on the providers’ storefront and you’ll find all the info you need to make the right choice: a description of the company or lab, the type of service offered, the number of services previously performed, and reviews of previous users. Select a few that seem to fit your needs and ask for a quote. You can then directly communicate with the provider to get the order through and arrange the logistical details.

Science Exchange Storefront

The Science Exchange storefront, you will find all the information you need to choose the right provider, including ratings and reviews from previous users.

Science Exchange is democratizing outsourcing in academia by acting as a facilitator. They take care of the painstaking steps involved in such collaborations. This includes helping you find the service you need, setting a price, and helping with the financial transaction so you don’t have to deal with the billing department of each provider you work with.

Turning your lab into a CRO?

Science Exchange welcomes private and academic labs to join them by opening a storefront. This model is quite common for private company, used to retail storefronts such as ebay and amazon. But for academic labs this could be a game changer. At no cost, the lab can showcase its expertise to researchers around the world, and offer services for a fee. The labs increase their national and international visibility and get an extra revenue stream.

Academic labs are still far from the virtual biotech model, but many academic labs do see value in outsourcing part of their work instead of doing it themselves or looking for more traditional forms of collaborations. For instance, the choice of outsourcing is often valid for the one time experiments that require outside expertise, or when complex ISO standards need to be followed.

With the increase in outsourcing, research institutions and funding agencies need to realize that an increasing part of research will now be contracted out of labs. Academic labs in particular will have to design policies that accommodate the mismatch between the teaching mission of many research institutions and the race for research results of the highest quality. Outsourcing experiments could mean fewer opportunities for PhD student to learn new techniques. And acting as a provider could mean spending more time doing out-of-context science for others instead of being creative on their own. But it could also give students a great feeling of productivity and an insight of the business side of scientific research.

In the meantime, Science Exchange is growing. It is listing US-based service providers only but do have long-term international intentions.

Cellkulture, the electronic lab notebook for cell culture, closes

Screen Shot 2014-08-26 at 2.47.24 PMCellkulture (blog post), the electronic lab notebook dedicated to cell culture is closing. In an email sent to his users, Cellkulture founder Dave Pier, explains that all activity will be stopped on the 10th of September 2014:

We are very sorry to announce that CellKulture will be shutting down on 10th September. At that point, CellKulture.com will no longer be available and all data deleted.

It’s our top priority to help you during this transition. Please visit http://CellKulture.com before 10th September to export your data. […]

Unfortunately, the high turn over of startups over is common for such a young industry. New ideas are constantly being tried out and they sometimes do not meet the users or the funder’s expectations rapidly enough. A normal process, yes, but still a problematic phenomena for researchers wanting to adopt these new tools since hours are invested entering data in the tool are simply lost, and the precious data are left without a home.

Cellkulture however. is doing a good job at letting its users down easy. The user’s data can be exported and the project might soon be available as a free open source production so that users can continue with this platform is they wish to do so. Still, this highlights the need for clearer opt-out policies for these young data-based startups. The user’s data should be exportable at all times, and it should be made clear how to read, search or import the data to one of the competitor’s solutions. Ideally, this should be clear right from the start, when adopting a new tool, not when the ship is sinking.

Free cloud-based lab notebook: Hivebench

Screen Shot 2014-08-08 at 3.23.25 PMShazino, is with Zappy lab one of the rare developers of high-quality mobile apps for researchers. Shazino offers a lab timer, bacterial colony counter, a paper reference manager and a plasmid-sharing platform, all available on iphone’s iOS.

But Shazino’s flagship product is now a electronic lab notebook, that has a lot to offer: Hivebench. In direct competition with other cloud-based and user-friendly solutions such as Labguru and Labfolder, Hivebench is a serious contender. It offer all the basics of lab notebooks including advanced text editing, and integration of images and videos. And it comes with an iphone mobile app that allows you to view and edit the notebook entries on the go.

When starting an experiment, you first create the notebook that will gather notes from experiments of a project you are working on. When creating a new entry, a template is automatically suggested for you to help you keep your notebook as standardized as possible. There, you can enter what your objectives are, what samples and procedures you are running, and what were the results of the experiments.

Screen Shot 2014-08-07 at 9.36.24 PM

Hivebench lab notebook interface, with a suggested template.

Of course, there is no obligation to follow the template and a few interesting functionalities help you customize your notebook entries. For example, you can display schematics of well plates with a single click and Hivebench makes it easy to add lists of experimental steps that will be automatically accompanied of a checkbox.

A couple more advanced options are also there to give more dynamic documents: inventory and protocols. A list of reagents can be imported or added manually in the Hivebench database then easily referred-to in the notebook. If done consistently, it becomes easy to track each reagent and see when they were acquired, where they are stored, in what experiment they were used, and when they expire.

Screen Shot 2014-08-07 at 9.42.31 PM

Hivebench lab inventory, where all reagent details are listed.

Protocols can also be entered in a database then automatically included in the notebook, avoiding you to re-write routine protocols every time. In addition, similar to the protocols.io initiative, Hivebench allows users to store their protocols in a public and cloud-based repository. Any Hivebench user can then directly import protocols from the repository.

Screen Shot 2014-08-09 at 10.20.59 PM

Hivebench public repository of protocols.

Hivebench also comes with a task manager and a calendar to plan the experiments so that your entire workflow can be managed from this single platform. Collaborative functions are of course well implemented, allowing you to easily share any of the items created in Hivebench. Mobility is now also a must for an electronic lab notebook, and Hivebench comes with a free mobile app for Iphone and Ipads which allows everything from reading your protocols to editing the notebook, right from the bench.

Hivebench is free for up to 10 team members and provides up to 10 GB of cloud storage for free, which is a significant advantage compared to other platforms such as Labguru. Hivebench can also be installed locally, which can be reassuring and economically more interesting for larger structures.

Extracting data from plots, images, and maps with WebPlotDigitizer

Screen Shot 2014-06-12 at 1.14.41 PMIt is hard to understand why in today’s all-interactive world, scientific data continues to be represented as still, lifeless images. Sadly, the good old pdf or html versions of research papers do not allow us to extract and reuse the data represented as graphics. While we wait for publishers to finally bring interactive figures to publications, and for data to be more open an easily accessible, a simple and reliable method to extract data from graph would be great. Lucky for us, WebPlotDigitizer does exactly that!

WebPlotDigitizer is a free, online tool, that allows anyone to upload the image of a graph and extract the data. Here are the announced features of the version 3.2 (released in May 2014):

  • Web based. No installation needed.
  • Supports XY charts (even skewed and non-orthogonal), polar plots, ternary diagrams and maps.
  • Automatic curve extraction algorithms aid rapid extraction of a large number of points.
  • Generates data in .CSV format which can be used by any data analysis program like Excel, OpenOffice, Origin etc.
  • A zoomed in view on the side aids accurate selection of data points.
  • Free of charge and distributed under the GNU General Public License Version 3.

This is how it works. First load your the image image of the graph by a simple drag and drop from the webpage or by browsing through your files on your computer. The image can be a screenshot, or even a photograph captured by your webcam since WebPlotDigitizer supports .jpeg, .png, .bmp and .gif. You can then make simple adjustments to the images, flipping or cropping it to your liking. The first step of the analysis consist in defining the type of graph analyzed and calibrating the axis by assigning four points of known values on the axis.

Then comes the extraction of the data points. A manual and an automatic mode are available. In the manual mode, you click directly on the graph to add data points and WebPlotDigitizer calculates the precise coordinates of each point. Simple and reliable but can be time consuming.

The automatic mode uses an extraction algorithm that will automatically identify and extract data points from the image. A few of parameters must be played around with to pinpoint the line or points that you wish to extract. The data can then be exported as a .cvs file or directly plotted using Plot.ly, a web-base graphing tool. The integration of WebPlotDigitizer in Plot.ly really differentiates this tool from the many other solutions, making plotting and sharing the extracted data incredibly easy.

Here are a few useful links to get you started:

And do not hesitate to make a donation to Ankit Rohatgi, creator of this wonderful tool, go to his website and click on donate!