1. Online tools for researchers
Vladimir Teif
08/02/2018

2. …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

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

4. Citing literature references
EndNote (for Windows and Mac)
Papers (for Mac)
Mendeley (online, needs registration)
Authorea (online, text editor and citing)
Many other solutions:

5. 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).

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

7. 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

8. Personal Google Scholar profile

9. 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

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

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

12. Not all papers will be cited

13. 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Journal peer-review does not guarantee the quality of the work, and many publications are even not peer-reviewed (e.g. preprints)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

14. 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

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

16. Biological preprints are on the rise

17. Ask your supervisor first!

18. 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

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

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

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

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

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

24. 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!)

25. Online networking

26. 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)

27. Do not do like this professor:
Name removed
Name removed

28. 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:

29. ~200,000 scientists on Twitter
… form a small, strongly connected community

30. 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!

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

32. 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”

33. @gene_regulation account

34. @gene_regulation audience:

35. @gene_regulation audience:

36. Typical twit statistics

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

38. 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)

39. 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

40. 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.

41. 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

42. E-notebook popularity?

43. Our experiment with LabArchives

44. 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…

45. See you online 
Web-site: generegulation.info