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README.md

Build a twitter literature bot in three steps

These instructions tell you how to set up a literature bot that automatically posts papers on particular topics to twitter/tumblr. We'll use the building of https://twitter.com/phy_papers as an example. It takes about 20 minutes.

Literature bots can be an extremely useful way to keep up with the latest research. Casey Bergman started it all with a Drosophila literature bot called flypapers, and there are now getting on for 200 similar ones (many built with the instructions below). Most of them can be found on this list: https://twitter.com/caseybergman/lists/literaturebots/members

Here are some very detailed instructions to make your own literature bot. These notes are inspired by Casey Bergman's blog post here: http://caseybergman.wordpress.com/2014/02/24/keeping-up-with-the-scientific-literature-using-twitterbots-the-flypapers-experiment/

The three basic steps

1. Set up a twitter account

  1. Decide on a name. A suggestion for consistency (following flypapers' lead):
    • "Full Name": something followed immediately by 'papers' (e.g. flypapers, phypapers)
    • "Username": the same as "Full Name" but with an underscore (e.g. fly_papers, phy_papers)
  2. Go here: https://twitter.com/
  3. Follow the links to set up your new account:
    • Protip 1: you don't necessarily need multiple email accounts. If you already use your gmail address for a personal twitter account, you can just append to it to create a new account. E.g. if your personal account is porcelain.crab@gmail.com, you could use porcelain.crab+phypapers@gmail.com (the '+' stays). I have 4 twitter accounts on the same email address like this.
    • Protip 2: you have to churn through some frustrating steps when signing up. The final one looks like you're going to have to import all your contacts. Just look for the very small 'skip this step' link at the bottom right
  4. Sign in to your new account, and stay signed in until you're done with these instructions
  5. Suggested: make sure email notifications are turned off
    • Click on the egg symbol next to the "Tweet button" at the top right
    • Click 'settings'.
    • Click 'Email notifications'.
    • If it says 'Email is enabled', click the 'Turn off' button

2. Set up a pubmed search

  1. Go here: http://www.ncbi.nlm.nih.gov/pubmed/
  2. Type in your favourite search terms (e.g.: 'phylogen*', or 'goats')
  3. Click "search"
  4. Click the "RSS" link (with the orange symbol) just below the search box
  5. Set "Number of items to be displayed" to 100
  6. Click "Create RSS"
  7. Click the orange "XML" box
  8. Record the address in your browser's address bar (this example: http://www.ncbi.nlm.nih.gov/entrez/eutils/erss.cgi?rss_guid=1LU7YBGfC-yDnaYBUcYLivlvzqhgKnWemjak5n2h7PxDtGFoHp)

3. Set up your dlvr.it account

  1. Go here: http://dlvr.it/
  2. Follow the steps to sign up for a new account (NB: the same gmail trick that works for twitter works here too...)
  3. Click "Start feed"
  4. Paste the RSS feed URL (from step 8, above) into the "Source" box
  5. Choose Twitter as the destination, and authorise dlvr.it to post to your new twitter account
  6. Click 'Done'
  7. Now tweak the delivery settings:
    • Hover over the content of the 'Sources' box, and click the pencil that appears
    • Click the 'Feed Update' tab, my suggestions for settings are:
      • Feed update period: 30 minutes
      • Max items per update period: 1
      • Max items per day: 250 (that's the maximum for a free account)
      • Trickle: Newest items first

That's it. Your new twitterbot is running. Give it a bit of time (a day or two perhaps) to catch up with itself before you tell everyone about it. This lets it fill up with interesting papers, and also allows you to tweak the pubmed search if necessary.

Going a bit further

1. Adding a feed from arxiv preprints

  1. Edit this URL to include your search term: 'http://export.arxiv.org/api/query?search_query=all:[YOURSEARCHTERMHERE]&start=0&max_results=10&sortBy=lastUpdatedDate&sortOrder=descending', e.g. for this example: 'http://export.arxiv.org/api/query?search_query=all:phylogen*&start=0&max_results=10&sortBy=lastUpdatedDate&sortOrder=descending'
  2. Log into dlvr.it
  3. Under 'Routes' click your twitterbot. It might be called 'my new route' if you didn't rename it.
  4. In the 'Sources' box, click the '+add' rectangle
  5. Click the square orange RSS symbol
  6. Click 'add feed'
  7. Paste the link from step 1 into the 'Feed URL' box
  8. Set your other options as in point 7 of the dlvr.it instructions, above
  9. Click 'Save source'

2. Adding a feed from bioRxiv preprints

  1. Copy this URL, which is an RSS feed from all of bioRxiv http://connect.biorxiv.org/biorxiv_xml.php?subject=all
  2. Follow steps 2 to 8 in the arxiv instructions, pasting the biorxiv link into the URL box
  3. Under the 'Filters' tab, add your search terms (this example: 'phylogenetics, phylogenomics' and a few related terms)
  4. Click 'save source'

3. Adding a feed from PeerJ PrePrints

  1. Copy this link: https://peerj.com/preprints/index.rss2
  2. Follow steps 2 to 8 in the arxiv instructions, pasting the above peerj link into the URL box
  3. Under the 'Filters' tab, add your search terms (this example: 'phylogenetics, phylogenomics' and a few related terms)
  4. Click 'save source'

4. Post your feed to tumblr

A few folks on twitter noted that it would be nice to have this feed posted to a non-twitter venue too. Tumblr is a good option here. So let's make dlvr.it post our newly minted literature bot to a tumblr account too. I did this but found that almost no people ever looked at the tumblr, so I removed it. But here are the instructions if you care to use them.

  1. Set up a tumblr account here: www.tumblr.com
  2. Set the username and title to match your full name for twitter. In this case, I set both to 'PhyPapers'. So this particular tumblr account will be phypapers.tumblr.com.
  3. Go to your literature bot on dlvr.it
  4. Look for the 'Destinations' box, that right now just has your twitter account in it. Click '+add'.
  5. Click the 't' for tumblr, then 'connect to tumblr'
  6. In the popup window, click 'Allow'
  7. Choose the right blog. In this example, I select 'phypapers' from the drop-down menu, then click 'Select'
  8. In the window that's now open, click the 'Post content' tab.
  9. Click the 'post body' tick box (this will post abstracts too, which is fine on tumblr where there's enough space for them).
  10. Click 'save' in the bottom right.
  11. Now visit www.tumblr.com. Click the cog symbol at the top. Then on the right click 'Notifications'. Use the settings here to turn off all email notifactions from this blog (if you want).

5. Tweak, revise, repeat

Make sure you follow and check your own feed. If it seems like it's posting rubbish, go tweak the search terms. For example, I noticed that the search above, using 'phylogen*' in pubmed, gathers all sorts of papers that just happen to have estimated a phylogenetic tree. That's not what I want, since the focus of most of those papers is often nothing to do with phylogenetics. So I revised my searches to be more specific. I now use this:

phylogenetics OR phylogenomics OR "phylogenetic analysis" OR "phylogenomic analysis" OR "phylogenetic analyses" OR "phylogenomic analyses" OR "phylogenetic methods" OR "phylogenomic methods" OR phyloinformatics OR "phyloinformatic analysis" OR "phyloinformatic analyses" OR "phyloinformatic methods" OR "phyloinformatic methods"

Long and unwieldy, but more precisely targeted to my interests, and less likely to fill mine and other people's streams with content we're not interested in.

If you find any mistakes or omissions in this document, raise an issue on the github page and I'll fix it.

This is free to use and redistribute under a CC0 license.

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