The IEU epigenetics journal club meets 1-2 Mondays per month. Each meeting relevant papers published since the last meeting are briefly presented and discussed. This repository contains:
- presentations
- scripts for selecting candidate papers
- data files recording previous candidate papers and presented papers
Candidate papers are all those published since the last meeting that
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come up in a pubmed query (saved in "data/pubmed-query.txt"), OR
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cite a paper presented in a previous journal club (saved in "data/presented.txt") AND
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do not appear in journal whose name is in "data/blacklisted.txt" AND
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has not come up in previous searches but was not selected for presentation (these are papers are saved in "data/ignore.txt").
Run the following from the command line:
Rscript --vanilla scripts/generate-candidates.r
By default, the script will look back 30 days for new papers and save them to 'candidates.csv'.
These defaults can be changed, e.g.
Rscript --vanilla scripts/generate-candidates.r 60 jc.csv
Probabilities of interest can be assigned to papers using a simple script script/train-bag-of-words.py.
python script/train-bag-of-words.py
This will load the generated 'candidates.csv' file, calculate probabilities and save the result in a file called 'candidates-with-probs.csv'.
Once you have selected papers to present, add their PMIDs to "data/presented.txt" and add the list of papers to 'data/papers.csv'.