Scholarly communication and visibility for bioinformaticians
Lee Katz, Andrew Page and Nabil-Fareed Alikhan discuss how microbial researchers and bioinformaticians can make their work easier to discover without turning promotion into a second job. They cover institutional profiles, publication records, peer review credit, social media, personal websites and public code. They also suggest ways for researchers without publications to demonstrate their interests and skills.
Listen to Episode 66: Scholarly Communications for Bioinformaticians on SoundCloud
In this episode
Make the work discoverable
Academic communication is not the same as commercial marketing: researchers are usually trying to reach peers who already share their interests. Andrew contrasts relentless sales messages with scientists spending years on a paper and then releasing it without explaining why anyone should read it. A striking result buried on page 39 of a 50-page paper is not an effective introduction. Lee adds that government work can appear under an organisation’s name, leaving individual contributions difficult to identify.
The first practical recommendation is to improve an institutional profile. Nabil argues that academic and government websites are trusted places to appear in search results. A name, photograph and department alone tell a prospective collaborator or employer very little.
Maintain publication and researcher profiles
Google Scholar is presented as a quick next step for researchers with publications. Claiming a profile, checking which papers belong to you and verifying an academic email address can make the record more useful. Andrew notes that Scholar groups copies of papers from different locations and can help readers find a preprint when a publisher’s page blocks access. Nabil recommends merging preprint and published-paper records so their citations contribute to one entry.
The hosts also mention Scopus and PubMed as routes to finding authors, particularly through more targeted searches of the kind a librarian might use. ORCID offers a persistent researcher identifier and a record that can include employment, education, grants and peer review. Journal updates are described as uneven: some happen automatically, while others need manual attention. A pronunciation detour establishes that ORCID sounds like the flower orchid.
Record peer review, but consider the trade-off
In this 2021 discussion, Nabil describes Publons as replacing Web of Science ResearcherID and providing a way to manage an author’s Web of Science profile. Its main attraction for him is recording peer review: researchers can report completed reviews, or participating journals can pass the information through automatically. A record of journals and review counts supplies evidence of service for applications without relying on memory.
Andrew raises the commercial trade-off: researchers contribute data that a large company can sell back to their organisations in another form. Nabil notes that some journals can instead connect review credit directly to ORCID. The time involved makes recognition worth discussing: Nabil estimates at least three hours for a substantial review, while Lee says he can take two days.
Twitter, blogs and personal websites
Andrew describes Twitter as his route to papers, preprints and the wider research community, as well as a place to share his own work and podcast episodes. The hosts discuss conversations around publications, code releases and blog posts. For a contemporary example, they point to SARS-CoV-2 discussion and a paper in the journal Vaccines that attracted criticism on Twitter and was subsequently retracted.
Blogs provide more space for explanation. Phil Ashton, Titus Brown and Mick Watson are mentioned, alongside Phil’s discussion of Mash and John Lees’s writing about genome sketches. Useful posts need not introduce an original method; explaining how something works or whether it suits a particular purpose can be valuable.
A personal website can preserve a portfolio across jobs, but maintenance matters. Andrew recalls his former LaTeX blog. Nabil warns about outdated information and WordPress security problems, and discusses static sites, including GitHub Pages using Jekyll.
Let code demonstrate your skills
Andrew recommends a recognisable GitHub identity rather than an unrelated username that makes its owner difficult to find. A profile or portfolio can bring together work from different employers, where their policies allow it. Scripts should also carry authorship and citation information in their help output; Lee suggests options such as –help or –citation so users can see whom to credit.
Code does not have to be a polished package to be worth sharing. A small data-processing script or an R script producing plots can demonstrate practical ability. Lee explains that a supplied code link helps him assess what an applicant has actually done. Nabil argues that visible work can reveal both current skills and training needs, rather than leaving an employer with no evidence. Andrew adds that public development can connect people working towards similar tools.
Build visibility before your first paper
For researchers without publications, Nabil suggests deciding what they want to demonstrate: interests, technical skills or communication ability. Presentation slides and posters can be deposited online with a DOI, but organisational rules and co-author agreement come first. Sensitive details may need removing. Protocols can be shared through protocols.io, and code can go on GitHub, GitLab or Bitbucket.
If original work cannot be released, short explanations or reviews of other people’s papers are another option. A post can describe what was useful, how a method works or how it fits a research problem without disclosing a confidential project. The aim is to give someone concrete evidence of what interests you and what you can do.
Small signposts help people reach those outputs. The hosts recommend choosing two useful links for an email signature, adding relevant links to CVs and applications, and giving audiences a next step in talks or posters. Nabil puts his Twitter handle on title slides; the broader advice is to provide a preferred contact route rather than assuming people will find it.
Highlights
- 00:00:47 — Developing an online presence through small changes rather than constant promotion
- 00:01:56 — Why publishing a paper is not enough to communicate its main result
- 00:07:31 — Using an institutional profile as the first place researchers find you
- 00:08:48 — Setting up Google Scholar and checking your publication record
- 00:10:43 — ORCID identifiers, journal integration and manual updates
- 00:14:21 — Publons, Web of Science profiles and recording peer review
- 00:21:27 — Twitter as a source of papers and a connection to the research community
- 00:24:59 — Personal websites as portfolios that persist across jobs
- 00:28:10 — Recognisable GitHub profiles and authorship information in script help
- 00:32:39 — Choosing two useful links for an email signature
- 00:35:37 — Putting a preferred contact route on conference title slides
- 00:37:42 — Demonstrating skills and interests before having publications
In their own words
Don’t just do it without people knowing. You kind of have to check with all the co-authors that it’s okay to do that.
— Nabil-Fareed Alikhan, 00:37:42
Who is talking
- Lee Katz (host)
- Andrew Page (host)
- Nabil-Fareed Alikhan (host)
Also mentioned: Phil Ashton, Titus Brown, Mick Watson, John Lees.
Tools and resources mentioned
Google Scholar, Scopus, PubMed, ORCID, Publons, Web of Science, Twitter, WordPress, LaTeX, GitHub, GitHub Pages, Jekyll, GitLab, Bitbucket, protocols.io, Mash.
Questions this episode answers
Where should a bioinformatician start with an online research presence?
The hosts recommend improving an institutional profile first, then setting up Google Scholar if you have publications. A useful profile should provide more than a name, photograph and department, with routes to your work and other relevant profiles.
Why merge a preprint and its published paper in Google Scholar?
Nabil recommends merging the records so citations to the preprint and final paper contribute to one entry. Andrew also notes that Scholar can connect copies in different locations, helping readers find an accessible version.
How can researchers show their skills before publishing a paper?
They can share approved slides, posters, protocols and code, or write explanations of methods and papers they have read. Nabil stresses checking organisational requirements and getting co-author agreement before releasing shared work.
Is unfinished bioinformatics code worth putting online?
The hosts argue that useful evidence does not have to be a polished software package: even a small analysis or plotting script can demonstrate ability. Public work can help employers assess skills and help researchers find potential collaborators, subject to permission to release it.
Is maintaining a personal research website worth the effort?
A personal website can provide a portfolio that survives job changes, but the hosts caution about stale information and maintenance burdens. They discuss static sites and GitHub Pages as simpler options than maintaining a more complex site.
This page was written from a machine transcript of the episode and checked against it. Listen to the episode for the whole conversation.
Show notes
Have you ever read a paper and wondered why the author buried their key result on page 39 of a 50 page paper? Bioinformaticians aren’t great at communicating themselves or their science to the wider world, so we have a chat about it, specifically with bioinformaticians in mind.
Topics include: Online presence/ scholarly communications for bioinformatics Google scholar/Scopus Marketing to a set of peers organisation websites managing publication record librarians citation metrics peer review twitter blogs personal webpage github for personal webpages sign up to github –help citation and name making your code public as you develop it. links in your signature self promote at end of slides just starting out
Links: How to pronounce ORCID - https://info.orcid.org/how-should-orcid-be-pronounced/#:~:text=But%2C%20for%20those%20who%20want,pronounced%20%E2%80%9Coar%2Dkid%E2%80%9D. Phil Ashtons blog: https://bitsandbugs.org/ Publons: https://publons.com/about/home/