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.

SciCurve: revealing life science’s curves

Screen Shot 2014-09-25 at 11.00.18 AMAfter the recent launch of Sciencescape, here is  another startup pledging to help us cope with the enormous amount of data and literature at our disposal. SciCurve uses PubMed‘s library of 23 million references to generate visually pleasing graphs and curves that helps you grasp trends in literature.  It comes with three main functionalities

Observing trends for your field of study.

For academic researchers, knowing about the publication trends in a field is fundamental when writing a review or a grant proposal. Is this field new? Has is been prolific in the 70s and is coming back? Or is it the latest hot field and is in exponential growth? SciCurve saves you the trouble of going through PubMed results and manually copy/pasting the number of search results. Simply enter one or more keyword and it will display a timeline of the number of publications and citation counts over the past 14 years.

Her's an exemple of teh trend function, showing an increasing number of publication since 2000, which is followed with an exponentially increasing number of citations.

The number of publications and citations for the keyword “biomaterials”. The raising  publication count since 2000 is followed by an increase in the number of citations.

 Exploring research networks.

One particularly challenging task when exploring the literature, is to quickly find the key papers, on which most of the field is based. Manually going through papers and tracing back the original work is time-consuming, and the large amount of information gathered could end up be confusing. SciCurve helps you analyse the literature automatically and helps you understand its findings by generating representations of how paper are interconnected.

The network tab displays a map of the network of publications based on citation relationships. Important papers tend to form nodes from which radiates the papers citing that work. Key papers, and the articles citing them can then easily be identified.

Example of a networks graph, with Biomaterials as a keyword.

Example of a network graph, with “biomaterials” as a keyword.

Second, the map function places on a map top papers of the field represented by circles of size proportional to their relevance. SciCurve clusters similar papers together, naturally point-out relevant sub-fields. This is particularly useful to understand what a field might entail.

Example of a map view with the keyword "Biomaterials" Clusters form show that sub-categories such as collagen, surface and engineering are prominent.

Example of a map view with the keyword “biomaterials”. Clusters reveals  sub-fields such as collagen, surface and engineering.

Finding who drives the scientific endeavour?

SciCurve also automatically generates author profile pages, including a map of their most frequent co-authors and a list of their publication. Wondering who are the most prolific authors in your field? SciCurve can identify the key authors in a particular field and map them out as a function of their publication record.

A map of the most published authors in the field of biomaterials

A map of the most published authors in the field of biomaterials

The graphs and maps, but not the raw data, can be downloaded in the free version of SciCurve. An enterprise version, with more advanced functionalities is offered for a fee. SciCurve also supports Zotero and Mendeley integration which allows you to easily export  references to your favorite citation management tools.

Beyond a rather obvious usefulness for academics and R&D scientists, this sort of tool could be interesting for general practitioners and other medical specialists that do not have the time to grasp the latest trends in medical research. Publishers and research databases could also use this approach to improve their search engines by providing a more data-rich and more visual experience to their users.

Sciencescape offers a new approach to searching for scientific publications

20202At the pace research is advancing, researchers must keep up to date with an impressive flow of information. Millions of papers are published every year and millions more are already available. So how can we stay up to date with the latest advances in our fields? And when exploring new areas of research, how can we identify the important papers that will help grasp the field quickly? Many great online tools such as  PubChase, Scizzle and scientific search engines such as Google Scholar, Pubmed and Web of Knowledge will all help you find and collect scientific papers. And you can now count on Sciencescape as well.

Sciencescape is a new way to discover and gather scientific publications. It uses the power of full text mining and network theory to help you find papers highly relevant to your search and interests. Sciencescape was founded over 3 years ago, however their public beta version was launched just this July. So lets have a look at what this new tool offers.

Sciencescape ranks paper a bit differently

Sciencescape ranks papers not by impact factor of the journal it is published in or citation counts, but based on their Eigenfactor. This elaborate method derived from network theory, gives a more detailed representation of the impact of scientific papers by taking into account not only the number of citations, but also the impact of the paper the citation is coming from. This technique is similar to those used by Google scholar and Google search: the more links point to a particular page, and the more important are the sites linking to that page, the better ranked the page will be. Enhanced by a few customizations special to Sciencescape, this Eigenfactor-based ranking brings up lists of highly relevant results.

Sciencescape

Publications are sorted by Eigenfactor, an alternative to citation numbers.

Browse networks of interconnected papers.

Beyond paper ranking, Scienscape makes the discovery of new papers easier and more efficient. With the approval of dozens of publishers to mine the full text of their research papers, Sciencescape extracts relevant information that helps link papers together by fields. As an example, for one of my publications, describing the use of mucins glycoproteins to pattern mammalian cells on surfaces, Sciencescape identified a dozen different fields (see screenshot below). Some of these are more relevant than others, but overall, Sciencescape is doing a fine job at identifying the scientific fields behind each paper it analyses.

Screen Shot 2014-07-18 at 9.30.42 AM

Scientific fields identified by Sciencescape from the full text mining of a paper.

You can then subscribe to the fields that interest you to receive updates about the latest papers in that particular field. Clicking on the field name leads you to the field chart page. The charts represent the publishing landscape for a certain field over time. Spikes in number of citations in open access journals are easily visualized. This makes it easy to spot the papers that are likely to be important in a particular field.

Screen Shot 2014-07-18 at 9.45.00 AM

Field charts help you get a glimpse at the most impactful papers in  a particular field over time.

A paper by John Smith? What John Smith?

Properly identifying authors can be a tricky task, mostly due to the relatively high occurrence of homonymes. The ORCID project is already well underway to solve this issue and by providing each researcher with a unique ID number to track their career and publishing records. Sciencescape takes an alternative approach by compiling the large set of information they have at their disposal to properly identify authors and their list of publications. This method does not require any effort on the author’s side, so it becomes easy to explore the publication records of any of your colleagues

The author description page automatically generated by Sciencescape

The author description page automatically generated by Sciencescape.

Don’t be selfish, share your findings within Sciencescape

Sciencescape is even more powerful when used within a community (think department or lab). Papers and collections are easily sharable and can be “broadcasted” to other sciencescape users via quick tweeter-like messages. By signing up with your institute’s email, Sciencescape can identify your Institute and connect you with your colleagues. These reference collections will soon be transposable in several mainstream reference managers such as Mendeley papers and Endnote.

How much?

The service is free for citizen scientists and academics and come at a fee for researchers working in the industry. This tool is still in beta testing phase, so expect changes in the interface and the addition of many new functionalities. But it is already a well build platform with a rather innovative approach to literature search, and I recommend checking it out!

Manage references from the comfort of your browser with Paperpile

Screen Shot 2014-02-16 at 8.18.46 PMPaperpile is a web-based reference manager that works with Chrome and Google Apps to help you find, organize, read, and write papers online. Another reference manager you might say? Well, yes. But for having tried it myself, I must say Paperpile is a solid contender. Let’s have a closer look.

Paperpile comes in the form of a Chrome App. This means that it is dependent on Google’s Chrome browser to function. It also heavily relies on Google Apps such as Google Docs and Google Drive. But as you will see below, this dependence is also its strength (if you can resolve to adopt Google’s services).

Start a collection of references – Like other reference managers, you start your collection by importing references from other reference managers, by uploading your pdf collection (that will be analyzed and added to the collection) or by browsing the web for papers. Paperpile is particularly well integrated in a number of scholar search engines such as Pubmed and Google Scholar. With one click, references can be added to your collection and the pdf downloaded. For those of you with limited access to pay-for-access journals, a neat function allows you to search for the pdf of the paper through Google search. An increasing number of pdfs are indeed available through repositories or personal websites. Newly added papers are automatically tagged as new, which makes it easy to come back to them after a long literature search.

Paperpile integration in Google scholar. Notice the Paperpile button on the right of the reference

Paperpile integration in Google scholar. Notice the Paperpile button on the right of the reference

Store your papers – Paperpile uses Google Drive to store all your pdfs, which makes them available to you wherever you are, including on mobile devices.  You won’t have to worry about running out of storage space with the 15Gb (30Gb on Google Apps for education) of free space Google Drive provides. Paperpile automatically renames uploaded or downloaded pdfs and organizes them in folders on the Drive. My paper collection was a bit messy but Paperpile helped put some order into it. It recognized a large majority of the pdfs I had, standardized the file names and arranged them in folders (thanks Paperpile :-D!).

pdfs can be accessed on mobile devices through Google Drive.

pdfs can be accessed on mobile devices through Google Drive.

Use your references – Once you are ready to write, you can use Paperpile with Google Docs to search your paper collection, include citations and generate a bibliography. Google Docs has a lot going for it: it has many of the basic functionalities other word processors have, is constantly evolving and is a great solution for collaborative writing. Google Docs can also be accessed and edited offline (but Paperpile will not work without internet connection). Still, at the end of the day, many prefer working with Word, and biology journals typically only accept Word papers. On this, Gregory Jordan, co-founder of Paperpile, said that integration into other word processors such as Word or Latex authoring tools is next on their to-do list. So wait and see!

Add references to you Google Doc manuscript.

Add references to you Google Doc manuscript.

Navigation in Paperpile – Navigation within paperpile is pleasant and the search function is very responsive. Articles can be given multiple labels that help organize papers by research field or project. Preset filters allow easy access to papers, book chapters or review articles of your collection. A ton of other small functionalities give Paperpile an overall mature and user-friendly feel.

You can give it a try for free for 30 days, then you are charged $2.99/month to use it. Paperpile is an initiative from a couple of researchers, Stefan Washietl, Gregory Jordan and Andreas Gruber that saw there was space to create a web-based reference manager that rivals the best desktop versions. And it seems they are very close to prove us right.

Scizzle, a new scientific paper aggregator

Screen Shot 2013-08-18 at 9.00.33 AMHere’s Scizzle, a new aggregator service for scientific articles. Scizzle was founded by Gaia Vasiliver-Shamis, researcher in immunology, after years of being frustrated with the un-efficiency of her literature search routine. She was simply tired of having her inbox flooded with tables of content sent by journals, having to go to different journal websites to look at the latest articles and setting publication alerts that just added more emails. Even after selecting the publications of interest, she ended up with a multitude of tabs opened, that stayed open, and often unread until the next browser crash.
So after “hearing a sigh every time I asked: how do you keep up with the literature“, Gaia created Scizzle, a central location  where scientists could aggregate the content they care about and easily organize, share and collaborate through an user-friendly and clean look interface. First, start by creating a series of feeds by entering a list of keywords. Scizzle will find 25 results from the past 30 days then automatically update the list on a regular basis. On a single page, one can navigate through the feeds, latest papers and paper abstracts. The abstracts listed can then be saved to an abstract collection, shared by email and their citations can be exported.

Scizzle is still in its infancy (~ 2 month old at the time of this post) with more functions to come soon. Any feedback from its users is appreciated.

Zappy Lab opens the way to mobile apps for researchers

Screen Shot 2013-06-09 at 6.55.39 PMI had the pleasure of meeting with Lenny Teytelman, co-founder of Zappy Lab a few weeks ago. He shared with me his vision for Zappy Lab: researchers will soon go mobile and there’s a need for good quality apps. The mobile apps for researches market is just emerging. A few journals,  search engines and life science companies already have their apps. Their are also a few simple apps that allows one to calculate dilutions and molecular weights.  I will very soon create a dedicated section for these apps in the “Online tools for researcher page“.

Zappy lab is the first company focusing on its mission to create an ecosystems of useful, practical and foolproof apps for researchers both in and outside the lab.They started with three simple but useful tools; a lab counter to count cell number at the microscope, another helps microbiologist keep track of bacterial growth curves, and a third app helps geneticists score yeast tetrad dissections.

Their flagship product is called PubChase, a tool to search, organize, and discover biomedical research. PubChase uses the PubMed database to allow users to easily search and browse through paper abstracts and to bookmark them to a personal PubChase library. Unlike other scientific search engines, PubChase generates recommendations for other papers based on the articles in your library, adapting rapidly to changes in interests you might show. This will be appreciated when starting new projects, especially when compared to other recommendation systems such as Google Scholar’s, that are based on citations. PubChase is available for both mobile devices (both iPhones and Androids) and web browsers.

The app is constantly evolving.  The web browser version now offers a free PDF cloud-storage to PubChase functions. Store up to 300 of your favorite articles for free and pay a subscription to store additional files. Many other functionalities are to come says Lenny, with the goal of creating a comprehensive and integrated suite of applications to support the researcher over the entirety of the research cycles (literature search, protocol development, experimentation, writing/communication).

Find, organize and discuss papers with Journal Lab

JournalLab_LogoJournal Lab popped-up on my radar this week. In a way, Journal Lab is similar to PubPeer since it allows users to post comment on research papers and start a discussion.

But Journal Lab adds a little twist to that by also enabling users to comment on specific figures. In the case of open access journal such as PloS, the figures are displayed along with the “reactions” and comments from readers. This might help start more targeted and clearer discussions.

Comment on article and article figures.

Comment on article and article figures.

Journal Lab goes beyond post-publishing reviewing and discussion by offering a “paper collections” functionality along with a convenient alert service. Journal Lab also introduces the concept of virtual journal club. With virtual journal clubs such as “RNA and Epigenetics” or “Active on PloS”, an exciting new paper is selected every week and opened for discussion.

Build a article collection and setup alerts.

Build a article collection and setup alerts.

Journal Lab was co-founded by UCSF graduate Robert Judson and social media entrepreneur David Jay in 2011. Find a recent interview by the UCSF student news paper here.

Search for facts buried in articles with EvidenceFinder

Europe PubMed Central has this interesting “lab section“, where they experiment new tools to improve how one can search their database.

EvidenceFinder is a search engine that digs deep into the full text of articles to find facts related to your search queries. EvidenceFinder then converts these facts into a list of questions. And for each question, corresponds articles containing specific answers.

For example, if I enter the keyword “mucin” (a glycoprotein, major component of our mucus), the tool will come up with a series of questions that I might have been thinking of:

  • What is bound to intestinal mucin?
  • What is bound by salivary mucin?
  • What degrades intestinal mucin?
  • What produces mucin?
  • What is inhibited by submaxillary mucin?
  • What dilutes in gastric mucin?
  • ….

Let’s say I was looking for information about what can bind to salivary mucin, the tool then displays articles that contain answers to the question. For example, here we learn that salivary mucin bins to Choleragen and “WGA” for example. The tool makes accessing very specific facts easy.

I found that the search had a very natural feel, probably because very often my search queries actually originate from questions. Usualy, I first mentally transform a question into keywords, then it is up to me to do the data mining. Here, the data mining is done for us, and the tool provides a list of questions that have been addressed in the literature. The service is still in the experimental phase, and is a bit to slow to be used in my every day search, but I will definitely be keeping an eye on this.

EvidenceFinder is developed by The National Centre for Text Mining (NaCTeM), a UK-based text mining centre that provides text mining services to the UK academic community. The tool is hosted by Europe PMC (formerly named UKPMC),  an initiative supported by 19 funders of biomedical research, including charities and government organisations in the UK, Austria, and Italy, led by the Wellcome Trust.

I will very soon create a new section in the “Online tools for researchers” page gathering the most innovative and useful research-oriented search engines.