Monday 9 April 2018

Some MAP kinase links...

I want to prepare a visualisation of MAP Kinase proteins in different species:
- probably fly, chicken, mouse and human as a starting point.

Search reveals these sources:

Evolutionary History of the Vertebrate Mitogen Activated Protein Kinases Family

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0026999

Evolutionary history of mitogen-activated protein kinase (MAPK) genes in Lotus, Medicago, and Phaseolus

these are plants - soya bean.

https://www.tandfonline.com/doi/full/10.4161/psb.27189

Wikipathways - chicken https://www.wikipathways.org/index.php/Pathway:WP769
Interpro: https://www.ebi.ac.uk/interpro/entry/IPR003527

UniProt search:

family:"protein kinase superfamily cmgc ser thr protein kinase family map kinase subfamily" AND organism:"Gallus gallus (Chicken) [9031]"

API Queries for UniProt

https://www.uniprot.org/help/api_queries

Uniprot search for:

protein kinase superfamily cmgc ser thr protein kinase family map kinase subfamily

Gives 205 protein entries across various species.

Go Ontology

https://www.ebi.ac.uk/QuickGO-Old/GTerm?id=GO:0004707

New article describing the tool, I used:

https://f1000research.com/articles/7-431/v1?utm_medium=email&utm_source=tracked_articles_alert

Authoring Bioconductor workflows with BiocWorkflowTools [version 1; referees: awaiting peer review]

Animal pics - Phylopic...

A search revealed this StackOverflow post:
https://stackoverflow.com/questions/28206611/adding-custom-image-to-geom-polygon-fill-in-ggplot
which led to rphylopic (https://github.com/sckott/rphylopic)

which seems interesting and relevant.

Link here to the parent site: http://phylopic.org/about/

Friday 6 April 2018

Grappling with writing a paper in RMarkdown...

I have submitted a manuscript to F1000Research as part of the Bioconductor Gateway. It's about drawProteins.

The workflow involved:

Writing text and code in RMarkdown using R Studio
Using BiocWorkflowTools (https://www.bioconductor.org/packages/release/bioc/html/BiocWorkflowTools.html)
Putting in citations from Bibdesk
Knitting with knitr in R Studio which creates multiple files...

A PDF
A tex file
A folder of latex figures (names not ideal, I think).

Uploading files to Overleaf
Logging into F1000Research
Linking into Overleaf
The uploading a Word file too (separate Rmd file and Knit required and some manual editing - WHY?)
Adding cover letter
Identifying referees - finding emails can be difficult!

A busy day of work...

Here are a few of the resources I used to help write the manuscript:

Visualisation and Data