Satoshi Village the blog of Daniel Himmelstein

University software licenses prevent reproducible science

Today is an exciting day for reproducibility in computational sciences. Continuous analysis awakens with its publication in Nature Biotechnology. Continuous analysis is a method for automatically re-executing a study whenever its source code is updated. Any changes resulting from the update are tracked and visible.

Once properly configured, continuous analysis makes a computational study fully reproducible at every state throughout its history. It works by combining two technologies. First, continuous integration monitors the source data …

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The most interesting case of scientific irreproducibility?

On February 26, 2016, the first version of an article titled “How blockchain-timestamped protocols could improve the trustworthiness of medical science” was posted to F1000Research. The paper had two authors: Greg Irving of the University of Cambridge and John Holden of Garswood Surgery. The article describes a method for timestamping clinical trials, so the retrospective existence of a trial can be verified at a later date. The technique uses the Bitcoin blockchain as an immutable …

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The licensing of bioRxiv preprints

Jordan Anaya of Omnes Res — creator of the PrePubMed search engine for biomedical preprints — recently compared bioRxiv 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 …

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My PhD Exhibit

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 …

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Four years of fellowship: annual summaries for my NSF Graduate Research Fellowship

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 …

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The history of publishing delays

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 …

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The preprint in 2015 and what comes next

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 …

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Electromagnetic pulses and slime molds

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.

Arguing the unforeseen

The year was 2010. I was …

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Publication delays at PLOS and 3,475 other journals

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 …

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My application to OpenCon 2015, the best conference ever

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 …

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