Knevel Lab Pages Repository

Website can be found at https://knevel-lab.github.io/

Guide to maintaining and updating

Group tab

Per individual the following information should be entered into the ~/_pages/group.html document:

• Square profile picture in .jpg format
• Small biography
• LinkedIn profile link
• GitHub profile link
• PubMed author search
• OrcID

See below for template block:

<div style="height: 150px;">
<img src="/images/Marc.jpg" alt="Marc Maurits" class="biopic">
<h2>Marc Maurits</h2>
PhD Candidate, pseudo-bioinformatician, expert in the field of being really picky and annoying about research, also website developer/maintainer
<br>
<a href="www.linkedin.com/in/marc-maurits-711889115"><i class="fab fa-fw fa-linkedin" aria-hidden="true"></i> LinkedIn</a>
<a href="/MarcMaurits"><i class="fab fa-fw fa-github" aria-hidden="true"></i> Github</a>
<a href="https://pubmed.ncbi.nlm.nih.gov/?term=Maurits+MP%5BAuthor%5D&sort=date"><i class="ai ai-pubmed-square ai-fw"></i> PubMed</a>
<a href="https://orcid.org/0000-0002-3266-6232"><i class="ai ai-orcid-square ai-fw"></i> ORCID</a>
</div>
<hr>

N.B. The <hr> could be omitted for the last entry.

Publications Tab

Per publication the following information should be entered into the ~/markdown_generator/publications.tsv document:

• Publication date
• Title
• Journal
• Short summary
• Short citation of the format Author, 1st. (Year) "title" <i>Journal</i>
• Short name for paper
• Link to paper

See below for example entry:

pub_date	title	venue	excerpt	citation	url_slug	paper_url
2020-05-27	Using genetics to prioritize diagnoses for rheumatology outpatients with inflammatory arthritis	Science Translational Medicine	short summary here	Knevel, R. (2020). "Using genetics to prioritize diagnoses for rheumatology outpatients with inflammatory arthritis" Science Translational Medicine.	gprob	https://www.science.org/doi/10.1126/scitranslmed.aay1548

The easiest way to alter the .tsv file is using a text editor that can visualise tabs (such as Notepad++)

N.B. avoid any symbols in the short summary as UTF-8 encoding will be enforced! (I use Notepad++ to convert to ANSI)

After altering the publications.tsv one should run the ~/markdown_generator/publications.py script to convert the new information to a proper entry.

Talks Tab

Per talk the following information should be entered into the ~/markdown_generator/talks.tsv document:

• Title
• Type of talk (oral/poster/postertour)
• Short name for talk
• Venue (e.g. EULAR 20xx)
• Date
• Location
• Link to talk
• Short summary

See below for example entry:

title	type	url_slug	venue	date	location	talk_url	description
EULAR 2022 Abstract EHR Clustering	Talk	talk-1	EULAR 2022	01/06/2022	Copenhagen, Denmark	http://exampleurl.com	Poster presentation of the work performed by Tjardo Maarseveen on the clustering of Rheumatoid Arthritis patients using baseline EHR data

The easiest way to alter the .tsv file is using a text editor that can visualise tabs (such as Notepad++)

N.B. avoid any symbols in the short summary as UTF-8 encoding will be enforced! (I use Notepad++ to convert to ANSI)

After altering the talks.tsv one should run the ~/markdown_generator/talks.py script to convert the new information to a proper entry.

Applications Tab

Per application the following information should be entered into ~/_pages/applications.html document:

• Title
• Link to GitHub
• Square thumbnail in .jpg format
• Short description
• Developer name

See below for template block:

<h4>Dx Extraction</h4>

<div style="height: 200px;">
<a href="/levrex/DiagnosisExtraction_ML">
<img src="/images/DxE_img.jpg" alt="Dx Extraction" class="applink">
</a>
<p>Pipeline for the extraction of diagnoses from free-written text fields in electronic health records.</p>
<p>Developed by TD Maarseveen</p>
</div>
<hr>

N.B. The <hr> could be omitted for the last entry.