Explain, enrich, and disseminate your research with Kudos

Kudos, is a UK-based company launched in 2013 that helps researchers and research institutions disseminate published research and increase its impact. Authors of published article can create a Kudos profile for their papers, providing an easy-to-understand summary and links to related documents.

So here is my first personal experience with Kudos. I took the last piece of work that I published this year. Kudos finds your published articles very easily, either after entering their DOIs or by connecting Kudos to your ORCID account.

Kudos then guides you through a series of steps. First, you need to choose a short title, free of technical terms. Ideally, the title should give the reader a mental image of what the work is about. The original title of my article was reasonably short : Covalently-crosslinked mucin biopolymer hydrogels for sustained drug delivery. But I made it a bit shorter and a bit more popular-science sounding: Medical device made of mucus delivers drugs.

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Paper profile page where the authors directly edits the short summary and links related documents

Then, you are prompted to write a little blurb about what the article deals with. Try to describe your work like you were talking to your friends that have no clue about scientific research. I’m not sure what it is worth, but here’s mine:

Drugs are often much more effective when delivered from inside the body,  slowly diffusing out from an implant. For instance, hip implants can release antibiotics to prevent infections, or gels loaded with anticancer drugs can be injected to kill tumors more efficiently. But designing materials that slowly release drugs can be challenging. A solution is to look towards nature. Polymers found in animals and plants are have plenty of interesting functionalities and are often well accepted by the body when implanted. Mucins are polymers that composes our mucus, the slimy gel that covers our eyes, nose, lungs, stomach, intestines, and the female reproductive tract. The mucus gel protects us from harmful particles, bacteria and viruses, by binding to them before they have a chance to enter the body. This sticky property is what we exploited here. We built a gel made of sticky mucins, loaded drugs inside the gel and measured their release over time. We saw that thanks to mucins’ stickiness, two very different drugs slowly released from the gel. For instance, antibiotics where release so slowly from the mucin gels that bacteria could not grow anywhere near the gel for over a month!

But you’re not done yet. What most people care about is not the how, it is the why. Why should I care? Kudos asks you to write a few lines about the significance of the work. Here’s my significance paragraph:

Although mucins are highly functional molecules and abundant in nature, they have not been used in technological applications. This article describes for the first time the assembly of mucins into a stiff hydrogel, and shows that their ability to bind certain molecules can be exploited for biomedical applications. This work should lead to other mucin-based biomaterials.

Finally, Kudos suggests that you provide a more personal view of the publication. This time, you are not speaking for all the authors, but just for yourself. I thought I would give my feeling about the paper and explain why I am excited and somewhat attached to it:

This is an exciting piece of work that I think could lead to many others. Of course, many challenges lie ahead before mucins can be used in biomedical applications. But as we move forward, we are learning about mucins’ fascinating properties and how to assemble mucins into functional materials that might have applications that we cannot foresee today.

OnScreen Shot 2015-09-03 at 12.05.58 PMce you’ve filled all of that in, you are invited to add links to any related documents. This is where you can link to an open access version of the paper in your self-archiving or institutional repository, add links towards related news articles or presentation slides that you might have shared on Slideshare. I linked a version of the article I stored on Zenodo and an infographic I’ve had made to explain the research through images.

The paper’s Kudos profile page is now complete! It will appear very similarly to the way it is displayed when you edited it. The way the summary is displayed could be improved a bit by making the screen a bit less dens in information, and by focusing a bit more on the text (which could use a slightly bigger font). I would also love to be able to add an image or two to illustrate the summary. But it still does the job!

Now that you’ve filled in all the requirements, it is time to share your Kudos paper profile with the world. You can link your social media accounts with Kudos, so that they help you spread the word. Or, you can get a short link and tweet it, mail it, or post it wherever you like.

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Disseminate your work through social media, or any other way by using a short url to your Kudos paper summary page.

Once it’s out, you can follow the impact of your Kudos paper profile on your Kudos dashboard. Through a collaboration with the Web of Science database and Altmetrics that tracks social media sharing of scientific articles, Kudos tell you how well your article is doing.

I’ve shared my Kudos profile on twitter and included a link in a post on LinkedIn and on Facebook and got these stats after a couple days:

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Hard to say what the impact on citations mights be in the long run, but I am guessing this kind of thing cannot hurt. On their website, Kudos claims that “in a pilot version of Kudos during 2013, researchers using the Kudos sharing tools saw an average increase in downloads of their publications of 19% compared to a control group”. Whatever the final outcome, this is a great platform to encourage researchers to start communicating about their research to a larger audience. It is easy to use, not too time consuming, and very importantly, Kudos rewards the researchers almost immediately for their efforts by providing metrics of how the Kudos profile and the article are doing.

6 digital tools for researchers added to the list.

Back after a short break with a series of new tools to the list of digital tools for researchers.

TScreen Shot 2015-08-28 at 5.26.50 PMhis is part of Elsevier’s SciVal platform, providing research institution and universities with research intelligence, including on their own research production. This service is only available through a subscription.

This service provide up to date news about research throughout the world, and alerts about funding opportunities. Also available through a subscription.

  • Screen Shot 2015-08-28 at 5.28.14 PMProfology – A professional community created exclusively for higher education faculty, staff and administrators.

A free social network for the non-students of higher eduction.The idea is to provide the staff with a more private space than what you might get on Facebook. Professor can share tip and trick about teaching or management of research groups without the risk of students bumping into it.

  • Kudos – Helps researchers explain, enrich and share their publications for greater research impact.

Screen Shot 2015-08-28 at 5.25.06 PMThis is good one. I will try to post a more extended post on Kudos soon. It provides authors with a space to explain their work in a way everyone can understand and link other ressources to the published article. A great way to increase the visibility of your published work.

  • Citavi – Reference management, knowledge organization, and task planning solution.

This Switzerland-based company offers a complete solution for your reference management. I have not tried it myself, but would love to hear from its users. Windows only for now.

  • InSIlico DB – Genomics made possible for biologists without programming.

This online platform seems like a great for those needing to use bio-informatic tools. It combines on the same platform an easy access to genome database with analysis tools. Have a look at this video from more info.

 

 

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