Last spring I went on parental leave and left science for what it was for more that three months. Writing new posts for this blog was something I thought I could do in my spare time, but soon I realized that taking care of my daughter was a full time job with very little spare time. In the end it was better like that.
Nonetheless, I kept on using twitter. Since most of the people that I follow on twitter are working in microbiology or in bioinformatics, I could at least keep myself informed on what was happening in these fields of science.
One of the more interesting things I discovered in that time, was that you can use twitter to update yourself and others on the latest scientific literature. I discovered this through a tweet which pointed me to the blog of Casey Bergman (An assembly of fragments). Casey is the owner of the twitterbot @fly_papers and he described in on of his posts how he set up this twitterbot.
What really struck me about the blog was that Casey had created the bot since he experienced an overload of papers filling up his mailbox, his RSS feeds, without the possibility to really keep up with the literature.
This sounded very familiar to me.
It has been ages since I looked at my RSS feeds via Feedly. My fear of the number of unread posts is keeping me away from it. It just takes too much time to go through it every week and check what is new. Because of that I felt already for a long time that I started to fall behind with what is new and hot in my research area and that I was not reading enough papers. I was just not motivated to tackle my rss feed updates.
And then I discovered twitter…
Twitter means for me a place to connect with other scientists. Many share their newest papers, ideas, hypotheses and importantly questions that they would like answers too. Twitter is also used to share the newest and most interesting scientific papers and I have now observed a few times that controversial papers end up being discussed on twitter and often debunked or send to the drawing board. Furthermore, people attending symposia , workshops or other meetings with an interest for a broader community post small bites from the meetings on twitter and those insights can point you to new ideas / results that are not yet in the literature. This makes twitter very interesting to me and others.
Of course the twitter streams are really like a river flowing past, and once in a while you check the stream to see what is happening. Trying to read all tweets is something I will not do and that would be too time consuming. But Twitter does help me to find new interesting papers and since they just flow by, I can just get an idea of if they are interesting to check or not.
So at some point when checking my twitter updates I saw the tweet from Casey on twitterbots. After reading the blog from Casey Bergman and the github page from Robert Lanfear I decided to set up my own twitterbots using the very detailed instructions from Robert.
I have only one note to Roberts instructions. It is true you can not use the same e-mail address for different twitter accounts, but when you use gmail that is not a problem. Within gmail it is possible to modify your e-mail address. So in my case I have my main e-mail address:
For a twitterbot I can then create the following e-mail address when signing up for a twitter account:
Twitter recognizes this address as a different address from my main mailbox. Gmail however will still collect the mails in my main mailbox. The handy thing is, in gmail I can filter out all messages for the twitterbot using the “+twitterbot” tag. Note that not all websites like this modification and will not accept the address.
So what bots did I create?
The first bot (@TTpapers) posts all Thermotogae papers found in both Scopus and Pubmed. I searched with ” Thermotog* ” at both databases. A little problem is that the Scopus database is behind a paywall.
The second bot (@Hvlife_papers) posts the newest publications on prokaryotic organisms connected to hydrothermal vents. For this bot I used a more complicated search since the word “hydrothermal” gives me a lot of nanotechnology papers.
This search is not yet optimal, but it is already giving me quite a nice list of papers. I will update this search in the next weeks.
My final twitterbot (@CrisprPhages) is checking pubmed for the latest publications on CRISPRs, phages and related topics. The search that I used is:
I made this search more specific by excluding papers on genome editing. I am not interested in the biotechnological applications of the CRISPR cas system so I try to filter those papers.
Using these three bots I already stumbled onto several two interesting papers:
At this point the twitterbots seems to be running and slowly they are posting papers. Not a lot of papers though. Roughly every two days a paper is posted on on any of these bots. So that is not too much hassle to check via Twitter of via Tweetdeck.