The new digital tools for scientific research

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Whether you’re a student, researcher or engineer, you’ve probably mastered to perfection certain IT tools: PowerPoint, word processing software, electronic messaging. Other, less well known tools exist, each with a specific use.  In research, as in many fields, it is important to organize one’s time and to use relevant, well-adapted tools. Do you need to organize your bibliographic search, exchange large files, or optimize your work as a team? The newcomers to help you with this are called ResearcherID, Figshare, Prezi and Sozi… Do you know them? Read on for a look at the digital tools to use for your scientific research.

 

This article is the english version of Les nouveaux outils numériques pour la recherche scientifique of  and is also part of our growing dossier on Scientific Social Networks, translated from the French by Abby Tabor.

 

Managing your bibliography and your literature review

Our article on tools and search engines for open access literature reviews (in French) has been the most read article on the MyScienceWork blog since September 2011. This considerable interest seems reason enough to draw up a list of the various tools available to researchers.

The first step of the process is the literature review.  It can be done in a systematic way, monitoring key words via Google Alerts, or with RSS feeds from journals, which can be easily managed thanks to feed aggregators like Google Reader and Netvibes. It can also be more selective. We usually use the term “curation” for the selection, by individuals, of relevant, high quality articles from among the mass of available information.  Social networks, too, allow for a collaborative review of the literature and sharing of bibliographies (See our article “Les Réseaux sociaux pour Scientifiques”; English version coming soon.)

The old-school bibliography (Credit: gadl/Flikr)
Bibliography

Next, managing one’s bibliography is at the center of research activity. Clearly, over time, the list of articles read and cited becomes significant. Tools for bibliographic management allow you to handle online, or on your computer, lists of publications and their associated files, generally in PDF format. These digital tools offer the possibility of automatically generating footnotes and bibliographic references according to various publication formats: Nature, Science, PNAS. Today there are some 20 choices of bibliographic software whose properties have been referenced on the Wikipedia page, Comparison of reference management software. Most will let you export the information relative to a publication directly from the websites of scientific journals (Nature, Cell, PLoS…) and databases (Web of Science, Pubmed, ArXiv, Google Scholar, IEEE Xplore, CiteSeer, Science Direct, WorldCat).

The most commonly used programs are probably EndNote, RefWorks, CiteULike, Papers for Macintosh and JabRef, which manages references in BibTex format for the document preparation system LaTeX. Only JabRef is free and developed in open source. Purchasing Papers and EndNote costs, respectively, 80 and 300 dollars and the RefWorks license, 100 dollars per year. The use of EndNote is certainly more widespread, especially at medical and pharmacy schools that appreciate its high level of security. (EndNote is a local program, used offline.) In addition, it allows for the management of larger databases and offers institutions licenses at reduced prices for their students and researchers.

Mendeley and Zotero are two other highly used tools. Entirely online, they also offer social functionalities: sharing of bibliographies and PDF documents, annotation of texts. They can also automatically generate bibliographies compatible with other formats of reference storage (EndNote, BibTeX), as well as document preparation programs (Microsoft Word, OpenOffice, LaTeX). Applications for iPhone/iPad are available and Zotero, developed in open source, is also available for Android.

Mendeley and Zotero encourage communication between scientists around the sharing of bibliographies and references.  Sharing the literature review, otherwise known as curation, is an activity found also on certain generalist social networks, particularly Twitter. This use is relatively more common in English-speaking countries. It encourages interdisciplinary exchanges and places the user at the center of a community with common interests, sharing their research monitoring efforts.

Digital software, the basic tools for a doctorate in research. © Steve Young - Fotolia.com
PhD student

Optimizing Teamwork

Research is rarely a solitary activity. Meetings and brainstorming sessions set the tempo of life in laboratories. Little by little, certain simple, common tools have been adopted there.  Colwiz, for example, is a bibliographic management program associated with calendars, agendas and several tools for efficiently managing schedules. Among the most classic, Google Calendar lets you share group agendas, and Doodle helps with planning events and meetings, or with opinion polling your working groups. Sites for content sharing, like Dropbox, simplify the exchange of bulky documents. This software, like Google Docs, lets researchers work on documents in parallel, simultaneously drafting, for example, a text.

Data and Content Sharing Platforms

This trend is generally referred to by the two terms open data and open science.  It aims to make scientific data available online so that they can potentially be reused. It is also an initiative with the goal of greater transparency, an objective shared by Open Data, a site that, since December 2011, brings together public data from the French government. Similar efforts exist around the world, in the United States and Great Britain, for example. Several scientific disciplines, like genetics and social sciences, are trying their hand at open data. However, the sharing of data still faces major technical difficulties, in addition to being held back by scientific competition. Documenting results in a complete way (experimental conditions, configuration parameters for measurement devices, etc.), in order to make them accessible to others, is a long and complex task. Still today, this process needs to be rethought and standardized.

A more specific tool, SciVee, lets you share scientific videos and podcasts. It encourages the sharing of recorded lectures, a practice occurring more and more frequently. To accompany research activity step by step, there is myExperiment, a collaborative environment for sharing workflows; that is, everything in connection with the different tasks of the research process. Figshare recently began offering a service for sharing research content, the entirety under a creative commons license, and SlideShare makes available visual materials from lectures and conferences.

For scientists with considerable amounts of data to exploit, it can also be interesting to invest in a citizen science project. This term includes serious games, like Foldit, and collaborative science projects, like Zooniverse.  As for the Kaggle project, it proposes turning the analysis of data into a competitive sport.

The Unclassifiables

Completely on its own, ResearcherID is an excellent site whose objective is to standardize the identity of authors of scientific publications. It assigns each author a unique identifier, which eliminates the ambiguities of different formats (first name, last name; initials, last name; initials of all first names, last name; etc.) This particularly improves the calculation of research evaluation factors: H-index, number of citations, etc. With ResearcherID, one can manage his or her identity on the internet and complete a detailed professional profile.

Use efficient digital management systems to avoid drowning in data.
email management

A program that needs no introduction, Microsoft PowerPoint is the presentation software par excellence. Beamer, on the other hand, is the program of LaTeX users. But there is also new software (Prezi and Sozi, for a free, open source option) that let you animate presentations with visual effects that grab the attention of your audience – ideal for reinvigorating a subject already hashed out many a time. They are also very interactive and adapt particularly well to sharing on the internet.

Nanopublication: Popularizing research for better visibility

Scientific blogs first appeared essentially in English-speaking countries. They are generally led by one or several researcher-bloggers who carry out a literature review and discuss subjects and results via their posts.  This practice encourages the diffusion of scientific knowledge.  It contributes to building the e-reputation of these scientific professionals and gives them a forum to make themselves heard. Indeed, if the spread of knowledge is important to ensure a better public understanding of the stakes involved, it is also fundamental that experts speak openly about complex subjects and state their position, in order to improve decisions made by administrations.

In English, ResearchBlogging and ScienceSeeker are probably the two most well known platforms, bringing together hundreds of posts from individual scientific blogs. In a similar way, since 2006, the c@fé des sciences has been offering a community of quality blogs published by French-speaking researchers and appreciators of science. As usage differs between disciplines, it is also worth noting, for example, the originality of the research logs and the social science platform of Hypotheses.org.

In a more general way, the term nanopublication covers all of the actions encouraging the diffusion of scientific results via the internet. Aside from blog posts, it includes messages on social networks – tweets and Facebook posts with the aim of inciting contacts to read a publication or to spread some information, thanks to just one or two catchy sentences. Our article “Twittos scientificus” assessed the uses for Twitter in research activities, by way of three different interviews. These sites known as social networks offer scientists practices that are helpful for building an e-reputation and for the visibility and accessibility of researchers on the internet.

All of these activities of collaborative work and visibility on the internet are modifying the functioning of research as they lift the veil on part of the activities of scientists. More exposed to criticism and comments, scientists are now taking back a central place in society. In the same vein, social networks dedicated to scientists (MyScienceWork, ResearchGate) have also appeared and will accompany the current opening up of science towards the international and the multidisciplinary. (See “Les réseaux Sociaux pour Scientifiques” on MyScienceWork.)

  To find out more :

MyScienceWork on Scoopit: Scientific Social Networks http://www.scoop.it/t/scientific-social-network

“Social networks for scientists” on MyScienceWork (article in French) http://blog.mysciencework.com/2012/04/02/les-reseaux-sociaux-pour-scientifiques.html

“Social Awareness Tools for Science Research”, D-Lib Magazine, the Magazine of Digital Library Research http://www.dlib.org/dlib/march12/mcmahon/03mcmahon.html

“Digital tools for the scientific endeavour – one response to the changing world of science”, In Verba, the blog of the Royal Society’s Science Policy Centre http://blogs.royalsociety.org/in-verba/2012/01/05/digital-tools-for-the-scientific-endeavour-one-response-to-the-changing-world-of-science/

“Twitter for research”, a Prezi presentation by Andy Priestner http://prezi.com/eb9huuoeikcp/twitter-for-research/

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Kael : I would just like to also mention GoLIMS, an online platform for conducting scientific research. Manage a project, write in your own digital notebook, control inventory, store files and also create presentations directly from your data. There is also a full audit trail, ability to share research publicly or to collaborate with your group. Follow us @golims to ask any questions!
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