This is a presentation I made to introduce undergraduate students to Scholarly communication and science 2.0. It has some examples of new tools that promote open data/access/...throughout the entire research pipeline.

1. Scholarly communication
Julie Decock, PhD
jdecock@qf.org.qa
QBRI summer studentship Program 2015

2. Scholarly communication
entire ecosystem through which research and other scholarly
writings are created, evaluated for quality, disseminated to the
scholarly community, and preserved for future use
Science 2.0
new generation of online-based tools that allows researchers to
change the way of scholary communication

3. scientific revolution of openness
Public perception
outreach
scientific output
Scientific community
collaboration
open data
open peer review and access

4. Kramer, Bianca; Bosman, Jeroen (2015): 101 Innovations in Scholarly Communication - the Changing Research Workflow. figshare.
http://dx.doi.org/10.6084/m9.figshare.1286826

5. Traditional pipeline
Tools requiring institute license

7. Open science pipeline
Tools accessible to researchers

8. Discovery

9. PubCrawler is a free "alerting" service
that scans daily updates to the NCBI
Medline (PubMed) and GenBank
(Entrez) databases using search
parameters specified by the user.

10. Analysis
Electronic lab books and
management tools
Bioinformatic tools

11. Ingenuity Pathway analysis (IPA) is a
commercial web-based analysis tool
to model, analyze, and
understand the complex biological
and chemical systems.
Some of its features are:
- structure & function of isoforms
- pathway comparison
- network analysis
- disease and biological function

12. Writing
Reference management
and sharing
+ PDF annotation

13. Zotero is a free and open-source
reference management software to
manage bibliographic data and
related research materials (such as
PDF files).
Some of its features are:
- web browser integration
- online library syncing
- library sharing
- in-text citations, footnotes and
bibliographies using word
processors

14. PaperShip is a tablet client for reference
management and pdf annotation.
Some of its features are:
- library syncing (Mendeley, Zotero)
- Pdf download
- Pdf annotation (highlighting, notes)
- Pdf sharing
- altmetrics

15. Pre-publication
copyright & self-archiving
Pre-print servers

16. Sherpa/Romeo is a website listing
publishers' copyright agreements and
retained author rights.
Copyright & self-archiving

17. bioRxiv is a free online archive for
preprints in the life sciences, enabling
authors to make their findings
immediately available to the scientific
community and receive feedback on
draft manuscripts before they are
submitted to journals.
A few journals will not consider
articles that have been posted to
preprint servers which can be found
on SHERPA/RoMEO.
Pre-print servers

18. Publication
Publication & Post
publication (peer) review
Open peer review

19. F1000 research is open access
publishing platform offering
immediate publication, open peer
review and full data deposition and
sharing.
open peer review

20. PubPeer is a website that allows
academics to engage in post-
publication peer review, and has
highlighted shortcomings in several
high-profile papers, in some cases
leading to retractions.
Post publication peer review

21. Retraction Watch is a blog that
reports on retractions of scientific
papers.
Post publication peer review

22. Data sharing

23. Figshare is an online digital repository
where researchers can make their research
outputs available in a citable, shareable
and discoverable manner, including
figures, datasets, images, and videos.
Data receive a permanent digital object
identifier (doi) which can be included in
the published paper.

24. Outreach

25. ResearchGate is a social networking site for
researchers to
- share papers
- ask and answer questions
- find collaborators

26. Assessment & impact
researcher identifiers and
author metrics
Altmetrics

27. ORCID (Open Researcher and Contributor ID)
assigns a non-proprietary alphanumeric code
to uniquely identify academic authors.
It is an open source web-app that allows
other web-apps to use its open application
program interface (API) and mine its open
data.
ORCID is adopted by
- Publishers (PLOS, Nature, Elsevier)
- Funders (Wellcome Trust, NIH)
- institutions
ORCID does NOT provide information on
impact.
researcher identifier

28. Google Scholar is a freely accessible web
search engine that indexes the full text or
metadata of scholarly literature across an
array of publishing formats and disciplines
including pre prints, theses, books, university
repositories, articles, …
The caveat is that as an author you need to
check for accuracy as it does NOT use a
unique researcher identifier.
Google Scholar does provide information on
publication impact, ie h-index.
author metrics

29. Impact Story is an open source, web-
based tool that measures the impact of
all research outputs, including journal
papers but also alternative research
outputs such as peer reviews
(Publons), datasets, presentations and
webpages.
Metrics include:
- # citations
- # mentions (twitter, blogs)
- # saves
- # views
Altmetrics

30. Science in transition