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SJfinder gets a serious update

SJFinder logoA group of scientists and technologists from Stanford University (US) and KU Leuven (Belgium) launched SJFinder in 2013 to help researchers find the right journal to publish in based on the title and abstract of their manuscript. Since then a number of new functionalities have been added to the site. The idea is to offer a collection of tools to researchers to give them more control over their networking and communication. 

Rate Journal SJFinder

Rate journals on SJFinder

Beyond the journal suggestions, SJFinder now also allow you to rate journals based on their reading and submission experiences. In an ideal world, submission would be chosen not on impact factor, but 1) on the traditional readership of the journal (if any) and 2) on the quality of the service provided by the publisher (i.e smoothness of peer review process, delay from submission to online availability, metrics on article, promotion of article).

SJFinder also helps you discover the literature, like other tools out there. In this case the simplicity of the user interface is especially appealing. Simply click on the fields that most interest you, and SJFinder will generate a list of the latest papers in that field. You can also subscribe by journal, but I personally think there something nice about exploring the literature by field and not by journal. Perhaps it is because it makes me less journal-biased and make it more likely to stumble upon interesting works and concepts.

map SJFinder

Find labs by exploring a map on SJFinder

To help you find new collaborations and showcase your work, SJFinder rolled out two other functionalities. First, an interactive map helps you find research labs anywhere in the world. You can brows the labs by research fields, location, or by keyword, and explore the map. You can also easily add your own labs to the directory. The benefit of having a world-wide database of lab displayed on a map is pretty clear to me. I would use it to find new local collaborations. Sometime a hallway is enough to separate groups that would otherwise collaborate wonderfully. Or to find laboratories that I could easily go visit while at a conference.

And second, SJFinder launched a drag-and-drop website builder to let you build a website for your lab. This will makes it possible for the many researchers with limited resources of time and capital to create a website and showcase their work. It might sound almost old fashioned, but in my mind a website is a must for any research group. This, along with other similar tools, are great way to get started at building your online presence.

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.

Report: Science Ecosystem 2.0: how will change occur?

book-933088_640The advent of Open Science and the digital technologies enabling open science is facing researchers with many changes in the way they are doing science, communicating science, and being evaluated. Connected Researcher does its part by helping researchers transition towards a more open and collaborative science by introducing them specialized digital tools.

But the European Commission, led by the commissioner for research, science and innovation Carlos Moedas, has also been very pro-active at looking at how the research and innovation ecosystems are being effected by digital technologies and other changes in organizational and work habits. They have launched major public consultation in the summer of 2014 and have now started to suggest rather ambitious policy actions (such as the launch of a common Cloud for researchers).

I was commissioned a report describing what the future of Science and innovation ecosystem could look like in an Open Science world. The report was commissioned as part of the activities of the Research, Innovation, and Science Policy Experts” (RISE) high level group. The mission of the RISE group is described on the EC’s website as follows.

RISE gives direct strategic support to the European Commissioner for research, innovation, and science and to the European Commission. It focuses on how to best use EU research, innovation, and science policy to address the European growth model and to create the conditions for a different type of growth, a growth that is smart, economically and environmentally sustainable, and socially inclusive for the EU and associated countries within a globalized world.

have a look if you are interested. The report is available on the European data sharing platform Zenodo: https://zenodo.org/record/33044

Five new tools added to the toolbox!

Ftoolbox-152140_640ive tools today added to the list today to hep researchers in their every day tasks. Find the complete list on the online tools for researchers page. I’ve also added a graph digitizer (dcsDigitiser) to the list you can find in this blog post.

  • Lab SuitInventory Management, orders Management, materials Trade-In, price Comparison.

So what’s “trade-in”? Well, it is simply opening up your lab inventory to other researchers. The more give away, the more you can ask others in return. A potentially great way to formalize the reagent exchange emailing list that most departments have.

  • Journal of Brief Ideas – Provides a place for short ideas to be described – in 200 words or less -, archived, searchable and citable.

This is based of the concept that ideas are common resource, and that it is only the way the idea is acted upon that should be attributed to group or individuals. Also check out the RIO journal that offers researchers to publish their research proposals.

  • SciFeed – Uses various data sources and natural language processing to identify important new scientific advances.

Probably a good way to keep on top of major scientific advances in all fields. This however won’t analyze your interest to suggest recent articles in your field.

  • LifeScience.net – Online platform for professional networking and sharing of knowledge in life sciences.

There, you will find a number of announcements related to the life sciences. Jobs, events, news, publications and protocols. Haven’t tried it myself.

  • F1000 workspace – A workspace for scientists to collect, write and discuss scientific literature.

The latest project from the F100 publishing platform. Check out the short video below.

F1000 – Writing Tools For Scientists from F1000 on Vimeo.

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.

Screen Shot 2015-09-03 at 11.22.37 AM

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:

Screen Shot 2015-09-08 at 11.13.55 AM

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.