From paper discovery to research group site with Labii

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

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

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

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

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

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

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

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

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

Pitchfest: Digital Science startup competition!

Screen Shot 2015-06-17 at 10.57.36Digital Science has been a driver in the nascent digital science industry. They have been  helping new ideas emerge and develop through networking events and their Catalyst Grant program.

Digital Science is now organizing a Pitchfest on the 14th of July 2015 in Cambidge, MA (USA). The concept? “Five early stage start-ups will each have five minutes to pitch their concept to an audience of peers and Boston based VC’s, with the winner bagging $1,500 in cash.

All early stage start-up focused on software for digitizing any stage of the scientific research process are welcome to apply. And for European startups similar event will soon be organized in London.

4 more digital tools for researchers!

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

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

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)