10 additions to the list of digital tools for researchers

format-indent-moreJust added a few new tools to the list of digital tools for researchers.

  • DeepDyve – Instant access to the journals you need.
  • Cofactor Science Journal Selector – A journal selector from the editing service Cofactor.
  • Journalysis – A service for academic authors run by academic authors for reviewing experiences with academic journals.
  • Biowebspin – Platform in life science worldwide to networks, work, look up information.
  • CaptoMe – A wealth of knowledge about clinical trials.
  • Research Connection – A searchable platform for research jobs and information.
  • Trelliscience – A digital platform that connects you to the rest of the scientific community, ran by the AAA.
  • GitLab – A git repository management, code reviews, issue tracking and wiki’s all in one platform.

We have also added a new section to the list: Fundraising/Grantwriting. This will include services that aim to facilitate fundraising, such as these two search engines for research grants.

  • Grant Forward – Search engine for research grants.
  • Pivot COS – A database which includes funding opportunities from all disciplines.


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.


Seven more tools to choose from!

Quick update of the list of digital tools for researchers. Interesting to see that this update includes two startups are offer remotely experimentation using  automated robots. The future is here!

  • TetraScience – Allows you to monitor & manage your experiments from anywhere.
  • Emerald Cloud Lab – A web-based life sciences lab, developed by scientists for scientists.

Two other are tools that scientists are increasingly using to increase their productivity.

  • Asana – Keeps your team organized, connected, and focused on results.
  • Evernote – A place to collect inspirational ideas, write meaningful words, and move your important projects forward.

And a few other in networking, peer-review, journal review, and  citation tools.

  • Piirus – Helps researchers meet potential collaborators, build networks and develop their core research.
  • Journal Review – Rate, and review published medical journal articles.
  • Journal Reviewer – Aggregates information users provide about their experience with academic journals’ review processes.
  • CitationStyles – Find and edit CSL citation styles.

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

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.

Digital tools for researchers update

noun_29406_ccI’ve added two new tools in the digital tools for researchers list. There are now over 170 tools listed!

I’ve added Biocompare in the Lab and project management section. This an impressive product comparaison platform for life science research.

  • Biocompare – Find products, read reviews and hear about the latest technological developments.

And I’ve added Scientific Protocols  in the Protocol repository section. This platform is part of the reproducibility initiative launched by a consortium of Digital Science startups (Science Exchange, PLOS, Figshare, Mendeley).

As a side note, I’m happy to say that Connected Researchers in seeing an increase traffic over the past few months. This is sign that researchers are in need of information about the digital tools at their disposal. There is much more we can do to guide researchers through this digital revolution. So do not hesitate to step up if you would like to contribute!

Happy new year to all!

(“Increase” logo Created by Rediffusion from the Noun Project)

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.

Ending authorship wars with a standard

Screen Shot 2014-11-14 at 3.32.30 PMIn research, most of the time this question does not come up until it is time to publish. Who did what? This question is essential, it will determine how authorship is distributed and ultimately how credit for the work is attributed. But very often, this information is not communicated, and although first authors are generally the do-ers and last authors the managers, there is a sea of unknowns between the two. This makes judging achievements based on authorship incredibly unreliable. PLOS journals and others already require precise descriptions of how authors contributed to the work. However terminologies can vary across journals, which prevents any real use of the information to assign credit.

In an attempt to solve the issue, the Wellcome Trust (Liz Allen) and Digital Science (Amy Brand) launched a new project called CRediT (Contributor Roles Taxonomy) last June. CRediT is now proposing a standard taxonomy composed of 14 defined roles such as “conceptualization”, “resources”, “supervision”, “writing – review & editing”… You can view them all here.

The CRediT project is now asking everyone to provide feedback on the taxonomy. If researchers show their interest in such a standard by helping to define it, there is more chance that journals will pick it up. And eventually that actual credit and career advancement are based on this system. So don’t hesitate to speak out your mind and spread the word.

The peer-review process under review with SciRev

SciRevI am probably not going to surprise you much by saying that the peer-review process of research articles could be improved. As I see it, peer-review should be an opportunity for researchers to improve their work. It should help detect flaws in the methodologies used and advise on how to improve the manuscript itself. But sadly, for many, peer-review feels like an unproductive waste of time, with sometimes endless waiting periods when the manuscript is in the hands of editors or slow reviewers. Even more frustrating is when the feedback consists of minimalistic reviews that bring little to the work. But things are slowly changing. Many journals now advertise their quick turn arounds and their network of competent and responsive reviewers. But with thousands of research journals in activity, it can be hard for researchers to know which journal is doing a good job at it and which are not.

SciRev is a platform that allows researchers to publish reviews of their experience with the peer-review process of specific journals. Facts including: the duration of the first review round, total handling time, number of reviewers, quality of the reviews, and an overall rating are displayed. A very useful “motivation” section also allows users to explain a bit about their experience with the journal. This usually gives interesting insights on the peer-review process. SciRev also allows you to compare several journal side by side.

Review of journals by users.

Review of journals by users.

The reviews seemed to be well balanced between the positive and the more negative. SciRev also gathers very valuable data that could help grasp the problems in the publishing sector. Based on the user data, SciRev also provides interesting statistics about the review process within various scientific fields (see below).

Rejection time and duration of the first round of review averaged for all scientific fields

This initiative, along with others that help researchers choose the right journals to publish in, will likely play a role in improving the publishing system. Indeed, the cost supported by universities associated with publication and with subscription to journals, should come with a matching service. For the price, we should expect services such as open access, innovative ways of communicating the research, and an efficient peer review process. Such journal-rating platforms could become key to identifying the journal that are ahead of the game.