Jordan Anaya of Omnes Res — creator of the PrePubMed search engine for biomedical preprints — recently comparedbioRxiv to PeerJ Preprints. We agree that PeerJ offers the better technology and user experience. However, bioRxiv has greater adoption in the biodata sciences.
In fact, since my last blog post on preprints at the beginning of 2016, bioRxiv has grown by 149% from 2,785 to 6,933 preprints. The growth has been fueled largely by the efforts …
1,700 days after moving to San Francisco for graduate school, I gave my thesis seminar. We live streamed the seminar on YouTube. The stream peaked at 20 concurrent viewers and had viewers from America, Bulgaria, Brazil, Britain, Canada, Czechia, France, and Israel. Here’s a shout-out to everyone who tuned in. If you missed it, the recording (below) and slides are online.
After the seminar, the Baranzini Lab organized a reception. The reception was …
As a first year graduate student at UCSF, I took a mandatory course titled Scientific Writing, which helped students apply for the National Science Foundation’s Graduate Research Fellowship. I was fortunate to receive the fellowship (Grant No. 1144247), which has funded the bulk of my PhD since its third year.
At the end of each fellowship year, fellows submit an Annual Activities Report, which includes a written Fellowship Year Summary. Below I’ve reproduced …
Last June, I released a summary of the recent publishing delays at 3,475 journals. The post attracted lots of attention via Twitter and Nature News, primarily because scientists are frustrated with the sluggish pace of publishing.
However, a major question remained. Are publication delays getting shorter or longer? Kendall Powell, writing a feature for Nature News released in tandem with this post, contacted me. Her investigation had uncovered a widespread belief that delays were …
2015 was a year of the preprint. While posting manuscripts prior to peer review and journal publication has long been practiced in physics, preprints are just catching on in the biosciences.
Last year, labs started universally preprinting, and preprints were billed as the solution to accelerating an ever more laborious publishing process.
To give some context, PeerJ PrePrints and bioRxiv both launched in 2013. Prior to 2015, PeerJ published on average 1.2 preprints per …
Recently I listened to a great podcast on the threat posed by electromagnetic pulses (EMPs). EMPs are short bursts of energy that can fry electronics. Large scale EMPs can be triggered by solar flares or high altitude nuclear detonations. A hefty nuclear EMP could destroy unprotected electronic equipment within a thousand miles radius. The podcast motivated me recount my strange story involving EMPs and slime molds.
On April 22, 2015 my research was formally accepted to PLOS Computational Biology. 68 days later the article has yet to be published. My current project builds on the forthcoming study and would benefit from its publication. Frustrated, I decided to investigate whether such delays are commonplace at PLOS.
Publication and acceptance delays at PLOS
I started by retrieving all PubMed records for the 7 PLOS journals. For each journal, I randomly selected 1000 articles …
Below I have posted the written portions of my application to OpenCon 2015, which was called the best conference ever by a 2014 attendee. This open science gathering will be held from November 14–16 in Brussels, Belgium. I have ordered my responses from practical to philosophical and mundane to radical.
For the events you checked, please explain how you plan to participate.
Last year I went to the Bay Area Open Access Week event …
We would like to thank Cancer Research UK for their cancer related advocacy and their coverage of our recent publication. However, we find several aspects of their interpretation troubling.
First, we find it unwise to discount our study because it analyzed counties rather than individuals. As Professor Pearce explains, much of our current understanding of cancer risk arose initially from ecological studies:
Historically, the key area in which epidemiologists have been able to “add value …
For the past two years, Kamen Simeonov and I have been working on a project codenamed The Lung. Today is PeerJ Publication Day and the results of our research are now online:
Simeonov KP, Himmelstein DS (2015) Lung cancer incidence decreases with elevation: evidence for oxygen as an inhaled carcinogen. PeerJ 2:e705 DOI: 10.7717/peerj.705
Findings
In this study, we investigated whether cancer rates varied with altitude. Our primary focus was lung …
