Online tools for researchers Vladimir Teif 08/02/2018

…for busy, skeptical researchers Dealing with literature: finding published works citing published works publishing your own research discussing and evaluating Social networking: increasing scientific visibility getting help and helping others Documenting and sharing your results electronic lab books collaborative writing online

Finding published works Scientific literature PubMed Google Scholar Grey literature: Google using advanced search

Citing literature references EndNote (for Windows and Mac) Papers (for Mac) Mendeley (online, needs registration) Authorea (online, text editor and citing) Many other solutions: https://en.wikipedia.org/wiki/Comparison_of_reference_management_software

Citation hints (PhD thesis) Avoid citing grey literature (anything except books, journals, preprints, theses). Pay attention to special styles when citing patents and legislation documents. Use Word + EndNote (free on campus). Can use alternative soft at your own risk, but make sure that your collaborators are also comfortable with the same software Always manually check citations (even EndNote makes mistakes). https://www.authorea.com/users/113502/articles/157923-a-student-guide-to-citations

Biomedical literature in PubMed Includes only peer-reviewed journals Advanced search (author, year, journal, etc) Not possible to track citations

Literature in Google Scholar Includes PDFs from all respectful sources (such as e.g. your personal web site ) Allows to sign up for search alerts It is possible to track citations Allows to create your own profile

Personal Google Scholar profile

Hunting for citations This is the most cited paper in the field; many recent papers will cite it We can’t read 18,900 papers

Let’s find recent citations Screening through titles of 74 papers is already realistic

Not all papers will be even read How to assure that people read your works?

Not all papers will be cited

The post-truth era in science Most published research is wrong (not a joke, see Ioannidis, PLoS Med 2005) Journal peer-review does not guarantee the quality of the work, and many publications are even not peer-reviewed (e.g. preprints) So what is the best predictor of the quality of the publication? Author’s reputation

Publishing your own research Peer-reviewed journals. You know this. Preprint archives for biology: arXiv.org – since 1991, all fields (LANL, CERN) bioRxiv.org – since 2013, only biology (CSHL) hal.archives-ouvertes.fr – since 2000 (CNRS) PeerJ, f1000research, Authorea, etc Publish both in journal and preprint  more citations for the same work http://arxiv.org/abs/1306.3261

Preprints are common in physics Biologists were historically less open, but this is changing

Biological preprints are on the rise

Ask your supervisor first!

University repository After 1st April 2016 we are required to submit all publications to the university repository within three months of acceptance This is needed for UK research evaluation (REF) Submit everything – the repository personnel will then sort out with copyright restrictions

Boosting your citations (2016) Use Proficio funds We’ll talk about this

Boosting your citations (poll repeated in 2017) Results are consistent with the 2016 poll

Peer-reviewer roles, really? Fine, if you can do this

Peer-reviewer roles, really? Most scientists agree to review almost all manuscripts they get Only few scientists can be selective in what they review

Don’t invest in blogs (?) Don’t trust, it’s a Twitter poll  These are good Don’t invest in blogs (?)

Academic branding online Start slowly (low risk, low gain): Upload your PDFs everywhere you can Update Wikipedia, re-write the history  Social networking (high risk, high gain): Create your nice profile Increase your follower base Post scientific updates (pictures!) Participate in discussions (accurately!)

Online networking

Professional behavior online Internet is addictive; keep track of your time Be professional, as if you are at a conference Usually it is not OK to criticize your employer Never use cursing, bad words. Never ever. Try not to mix personal and professional (most of your peers do not care about your cooking and your favorite sport team) Avoid discussing politics – it is divisive, spam (do discuss ethical issues and science policy)

Do not do like this professor: Name removed Name removed

Getting and giving help online Do ask questions online – this is normal Do help other people – it is good for you Do not forget to thank people! Examples of scientific Internet forums: https://www.biostars.org http://biology-online.org http://protocol-online.org http://molecularstation.com http://biotechniques.com http://seqanswers.com http://www.scientistsolutions.com

~200,000 scientists on Twitter … form a small, strongly connected community

So why using Twitter? Because ~10% scientists already use Twitter Manca S. and Ranieri M. (2016) “Yes for sharing, no for teaching!”: Social Media in academic practices, The Internet and Higher Education, 29, 63–74 Because ~10% scientists already use Twitter All scientists whom we invited to speak at our genomics conference are on Twitter Because it can be fast and effective: Technical questions are answered within several minutes or hours Conference or job announcement Because it is fun!

The best scientific web platform? Don’t trust, it’s a Twitter poll  The ideal scientific web platform still does not exist

Why scientists spend time online? I am having here a nice time and it is useful for my work 40% I am having here a nice time, relaxing after work 19% I am polishing my scientific arguments in online discussions 12% I am addicted to the Internet. I’d like to leave, but can not 10% I am getting here some useful information for my work 5% I am popularizing my scientific ideas/publications I am advertising my products/services I am helping other members, and I like it 2% I am maintaining contacts with my colleagues here I am here mainly to exchange PDF articles free of charge 0% Teif V.B., 2014, “On the sociology of Science 2.0” https://link.springer.com/chapter/10.1007/978-3-319-00026-8_23

@gene_regulation account

@gene_regulation audience:

@gene_regulation audience:

Typical twit statistics

Want to learn Twitter? Read more details here: http://generegulation.info/index.php/ open-science/scientific-twitter Questions? Email me anytime. Want to be our school ambassador? Want to be your group ambassador? Talk to me; talk to your supervisor

Online text editors when/why are they needed? Simultaneous editing of the same document Final document planned to be a web page Linked to collaborative programming project Collaborators use incompatible editors (e.g. MS Word vs. LaTeX)

Online text editor examples Google Docs: simple, popular, many add-ons MS OneNote: simple, functional, integrated with MS Office 365 (free for our university) Authorea and many other recent projects https://en.wikipedia.org/wiki/Comparison_of_text_editors

Electronic lab books: why/when are they needed? You work alone on your project (very rarely). In this case use a simple local PC system (for example, log all your activities in a Word file. B) You work together with collaborators (or your supervisor). In this case agree with all involved people, which electronic system to share information is preferred.

Electronic lab books Replacement of usual laboratory notebooks + e-signature, timestamps, collaboration… Exchange of bioinformatics workflows e.g. Taverna: start script A, then B… Exchange of experimental protocols protocols.io

E-notebook popularity?

Our experiment with LabArchives

Our lab’s experiment with LabArchives Every bit of science needs to be documented in lab notebook in real time Explain the rationale, why you are doing this Aim to write it first in the electronic lab notebook, then execute It allows you to spot mistakes before they affect your calculations Recording after calculation is a double-work and you may miss details OK, if you code really fast, write up immediately after the execution Our lab’s experiment continues…

See you online  Twitter: @gene_regulation E-mail: vteif@essex.ac.uk Web-site: generegulation.info