Automated pubmed searching with RSS

If you're regularly searching pubmed on a particular topic, you can make your life a lot more comfortable using automated searches. Everything that is required is a web browser and a RSS-aggregator, such as the soon-to-fade-out Google Reader, feedly, or a Tiny Tiny RSS instance (if you're geek enough to set one up for this purpose).

Here's how it works:

1. Go to pubmed.
2. Type in your favorite search query.
3. Click "Search".
4. After the result appeared, click on the button "RSS" below the query field.
5. Adjust the settings to your liking and click "Create RSS".
6. Use the xml-link to subscribe to this search in your favorite aggregator.

Et voila, you're done! Next time you log in to your feed aggregator, you'll see all the new articles that match the query. The cool thing is, you don't have to check the search on a regular basis anymore - your feed aggregator will keep track on all the new results as they tumble in via the feed. Unread items will be highlighted. If you use a mobile client, you can use the time on the train to browse through the list and star interesting articles for later reading. 

You can take this a step further, and subscribe to TOCs from your favorite journals. Never face a pile of unread TOC alerts in your inbox again. Every decent journal out there offers an RSS feed. 

Replace Google Reader with Tiny Tiny RSS

Google Reader was an essential part of my workflow for keeping up with the literature. I had configured several PubMed-searches as RSS-Feeds. For example, I created an automated search for olf*. Hence, every time a new article appeared on pubmed that contained that term, it would appear in my Google Reader. That was extremely convenient, as I could simply log in to Google Reader whenever I felt like reading new stuff, then browse the RSS with the pubmed query, star interesting abstracts, download those articles and push them to my cloud storage where I keep the PDFs. 
Now Google announced to shut down the Reader Service. Booooooh, bad Google! However, I can't afford to let the decision of some internet company disrupt my workflow ;) So I looked for alternatives, and found Tiny Tiny RSS. TT-RSS is a server-side application to be installed on some webserver. It provides similar service as Google Reader, and even an Android client!
It took me two hours to set it all up, including dusting off my Mysql knowledge and learning how to use systemd. I got along mostly with the install instructions from the TT-RSS website. The only thing which took some time was figuring out how to set up a MySQL database for ttrss, and configuring systemd to run the update daemon. In the end it was pretty straightforward. 

Now my workflow's saved! Happy! ;) 


Note to self: Here's the systemd-service file that is required to start the update daemon for ttrss. To enable it, store it at /lib/systemd/system/ttrss-update.service, and enable it permanently using systemctl enable ttrss-update.service.

[Unit]
Description=Update daemon for ttrss
After=network.target

[Service]
Type=simple
User=wwwrun
Group=www
ExecStart=/usr/bin/php /srv/www/htdocs/feeds/update.php --daemon
Restart=always
RestartSec=60

[Install]
WantedBy=multi-user.target

!!! Update!!! (April 12.2013): the script was missing a second hyphen before -update, which caused the update to be run exactly once on startup, and never again. Fixed.

Second Update Oct 30, 2013: Added Restart flag to the service that takes care of firing the update daemon up again if it exits.

Interview on Sciple.org

Sciple.org has published an interview with me. Sciple.org is a relatively new platform which is about people in science, with a special focus on young scientists. It also has a "Future" section with interesting graphs... still growing, but interesting to watch anyhow. That part reminded me a bit of Seed Magazine, a magazine about science culture, the print version of which I subscribed to some time ago and which I enjoyed quite a lot. I still read their RSS feed occasionally.

Any jackass can trash a manuscript...

It seems I'm not the only one getting hilarious reviews from time to time. The Journal of Molecular Biology of the Cell (MBoC) has published an editorial that speaks from my heart, titled "Any jackass can trash a manuscript, but it takes good scholarship to create one (how MBoC promotes civil and constructive peer review)".

In my opinion, one of the most important points in the article is that the relentless bashing which has become a recurring feature of many reviews will, inevitably, hurt the entire research field, because it destroys the scientific community in that field.

As I said before, I think that an open peer review process with identifiable reviewers will foster constructive criticism in the reviews. The reviewers will become visible and their contribution to the community acknowledged. The whole process will become more transparent, which is a prerequisite for a functioning scientific community.

SEED Magazine: The scientific paper is becoming obsolete

SEED Magazine, a New York-based magazine on science culture, just published an interesting article about how science publishing is about to be transformed by the internet. You might think that this is an old hat, and in fact the idea that the internet revolutionizes the way we publish and access scientific results is not new. Indeed, "the Internet" was "invented" by scientists to share knowledge. Yet still, subscription costs rise, although the price of knowledge dissemination via the internet is much cheaper than in printed media. The market has obviously failed. Access to scientific results has become expensive, so expensive that the main funders of science (tax payers) only rarely can access to the knowledge which is produced using their money.

More importantly, limited access to scientific results directly harms scientific progress. It is not unusual that it takes about two years until a paper is published. By the time a scientific breakthrough is published, it often fails to make real impact, apart from discouraging other labs to work in that direction.

The tools to overcome the limitations are all there: Scientific results can be published on preprint servers (like arXiv or Nature Precedings) right after writing them up. The stream of information coming out of those servers can be filtered by the scientific community by writing blog posts, or by commenting on the preprint servers directly. So why are these tools still so rarely used in life science?

The answer is simple: Lack of incentive. Writing blog posts does not extend my contract, papers on preprint servers do not increase my university budget (opposed to papers in high-impact journals), and often the possibility to publish in popular journals is compromised by publication on a preprint server.

However, incentive will rise as more and more researchers get frustrated by the corporate science publishing machinery. As more and more university libraries drop out from subscriptions as publishers increase their fees, researchers focus on open access journals. As it is becoming more and more difficult to publish in high-ranking journals, researchers consider alternatives which enable them to spend more time on research and less on getting bashed in anonymous peer review.

For example, PLoS ONE is very successful with publishing papers reviewed for technical correctness, but leaving it to the reader to gauge it's scientific impact. Recently, even Nature publishing group picked up the idea and started it's own version of PLoS ONE, Scientific Reports.

While these journals make it easier to publish one's findings, it is up to the researcher to make an impact in terms of influencing the field. Doing good research takes you only half way. The other half consists of convincing other researchers about one's ideas. The great advantage is that this process takes place in public, while in anonymous peer review it is hidden from the largest part of the scientific community.

PNAS Editorial: Impact Factor corrupts science

The (ab)use of the impact factor to evaluate the scientific merit of individuals corrupts the way how scientists publish their findings, say Eve Marder, Helmut Kettenmann and Sten Grillner in their recent editorial to PNAS. Moreover, they state that the current practice to measure scientific achievement shifts the choice of research topic to potentially "great discoveries" (read: discoveries which will make it to Nature), although the most important findings in science were made serendipitously, and hence the eventual contribution to science could not be estimated beforehand.

However, in my opinion, the impact factor is only the tip of the iceberg. Even worse is the implicit role of author sequence on a paper. In life sciences, the first author typically is the one who did the work, and the last author is the supervisor or lab head. All authors in between are perceived to be "minor contributors". Of course, this rule leads to all kinds of problems. Fierce battles are fought over author sequence, since for PhD students, only first-author papers count, while for group leaders last-author papers are vital to demonstrate their scientific contribution.

But there can only be one author first, and one author last. Of course, there are "equal contribution" asterisks all over the place, but are they actually been taken into account? After all, how much sense does it make to refer to the deprecated, intransparent and inflexible rule of author sequence to indicate contribution? For example, it is completely unclear how to handle interdisciplinary collaborations, which involve typically at least two PhD students and two group leaders.

A completely fair and unbiased way to state individual contributions to a scientific publication would be to list the authors in alphabetical order and have an "Author contribution" section in the paper, where the individual contributions are described in detail. In fact, this is how many disciplines handle it, for example in social sciences.

Paper on the honeybee brain atlas with 3D figures

Colleagues of mine published a paper on the three-dimensional atlas of the honeybee brain. This atlas is a collection of three-dimensional morphological data from honeybee neurons.

The honeybee brain atlas was first published in 2005 in the form of a conventional paper. It is extremely useful for research in a number of ways:

• For physiological recordings, the atlas helps you identify the neurons that you record from.
• The atlas gives you a common frame of reference to compare morphological studies from different animals, experimenters or even different labs.
  
• It allows to put different neurons from different specimens in spatial relation, which is a prerequisite for reconstructing neuronal circuits in the honeybee brain.
  

The caveat is that in order to use the atlas, one needs the whole software stack on which it was developed. Only those who have seen it in action can really grasp its significance. In consequence, the atlas was always a bit of an insider's tip within the honeybee brain community.

In their recent publication, Jürgen Rybak and coworkers made full use of the capabilities of the PDF format and published three-dimensional figures. The reader can interact with the atlas and rotate the brain for better overview, hide and show parts of the brain or even specific neurons. Now everyone can examine the bee brain in a way that was before only accessible to a small group of scientists. And since the paper is open access, you don't even have to pay for it.

Thanks a lot for that great piece of science!

Preprint servers vs. anonymous peer review

Recently, I got a manuscript rejected. There's nothing wrong with that, I consider rejection as a part of the publication process. Or more precisely, as a stop on the way to the publication of a manuscript.

But what really was annoying is that the reviewers did not even seem to read the manuscript until the end. They criticized the lack of a specific kind of information. But this information was explicitely elaborated upon in the discussion part. Even after pointing them to the exact paragraph where the information was given, they did not acknowledge it (let alone say whether this satisfies their criticism). And then it took them two months and several iterations back and forth to finally reach their conclusion to reject the article.

This experience goes along with what I hear from colleagues, namely that they seem to get more and more rude reviews. Constructive criticism appears to be a rare good in neuroscience nowadays. In addition, it is not uncommon that it takes a year or longer from the initial submission to the final publication of the manuscript.

One of my thoughts was that probably the concept of anonymous peer review poses a problem here. As the pressure to publish rises, so rises the number of journals. These journals require more reviewers, who get more papers to review. It becomes increasingly difficult to devote the necessary time and effort to judge a manuscript in its entirety. In addition, there is no way the reviewers' effort is honored when peer review is anonymous. Journals like the Frontiers in... series already act up by naming reviewers on the published manuscript, in order to get the reviewers' contributions noticed.

I would definitely welcome an open peer review process, where reviewers are named from the first revision on, and the reviews are made publicly accessible. Preprint servers like ArXiv are pretty much what I'd like to have in neuroscience. You put your paper there, you get comments, you revise the manuscript, and at some point a journal or a conference will accept it. Your knowledge is accessible right from the first upload on the server. Efficient exchange of scientific results favors the rapid advancement of the field. Moreover, it is much less likely that you get scooped during the review process, since you can always document when you published the paper for the first time.

I will evaluate possibilities for this kind of publication for the resubmission of my manuscript.

Yet another python primer

Another python tutorial, this time specially for life science researchers. Published back in November last year, but it took me until today to run across it. It seems to be focused towards bioinformatics, at least from what I can tell by quickly going through it. Might be useful for students entering the field, not knowing which lagnuage to learn.

Citation: Bassi S (2007) A Primer on Python for Life Science Researchers. PLoS Comput Biol 3(11): e199