Mapping the Long Trail: the best is now free with OpenStreetMaps| blog.dhimmel.com
On January 24, 2010, Zeke Farwell completed the Long Trail. He had begun just two days earlier, connecting more than 50 segments of trail spanning over 200 miles. Motivated by “the longest and most well known hiking trail in Vermont”, Zeke often revisited portions of the trails in the years to come. Now I’m not revealing a secret FKT, but rather the completion of the Long Trail route on OpenStreetMap. OpenStreetMap is like Wikipedia …| Satoshi Village
The John Maddox Prize has been awarded annually since 2012 to “researchers who have shown great courage and integrity in standing up for science and scientific reasoning against fierce opposition and hostility”. The prize is a joint initiative between the journal Nature and the Sense about Science charity. Fergus Kane nominated Alexandra Elbakyan, creator of Sci-Hub, for the prize in 2018. While selected to a final shortlist, she did not win. Dr. Kane has nominated …| Satoshi Village
Iceland’s longest continuous marked trail, some say. Where the night is not, the wind wails, the rain rages, and geysers gurgle. Starting June 15, 2019, I hiked from Skógar to Leirubakki in Iceland. My five day trek covered the following connected trails: Fimmvörðuháls Trail (Skógar and Þórsmörk, 24 km) Laugavegur Trail (Þórsmörk to Landmannalaugar, 63 km) Hellismannaleið Trail (Landmannalaugar to Rjúpnavellir, 55 km) Hellismannaleið Trail Extension (Rjúpnavellir to Leir...| Satoshi Village
Below is the saga of how it took six months and 75 messages for Uber Support to admit a billing error. The issue was quite simple. The receipt indicated that I paid via Uber Credits, however my credit card was charged for the fare. After countless hours of back-and-forth, Uber finally claimed that the receipt is incorrect. However, Uber has still not updated the receipt nor refunded me. On June 23, 2018, I took an …| Satoshi Village
This post discloses an 8-day itinerary for exploring the Big Island, Hawaii. It is based on the expedition performed by Trang and I in January 2019. Of our 7 nights off the resort, we tent camped for six, which kept the combined lodging costs under $250. Warning: these adventures are not for the weak. Instead, these feats should only be attempted by a strong and frugal traveler, who is prepared to leave no trace. We …| Satoshi Village
On Wednesday, June 27, 2018 I woke up in Zurich, having given a presentation at the Central Library the day prior. After 3 trains, I arrived in the French town of Vallorcine to begin my hike of the Aiguilles Rouges, which in English translates to “Red Peaks”. The beginning of the hike was picturesque with benign terrain (this would change soon enough): The first day was full of day hikers and alpine ibex (bouquetin in …| Satoshi Village
Should citations in scholarly writing appear as author-year snippets, like (Pantcheva, 2018; Zelle, 2015), or numbers, like [1,2]? Let’s refer to these two methods as author-style and numeric-style. You may have also heard them referred to as the Harvard and Vancouver referencing systems. Author-style Here’s an example of author-style from our recent Sci-Hub Coverage Study published in eLife. First, see how citations appear in the main text: Notice how studies with 3 …| Satoshi Village
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, ...| Satoshi Village
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 …| Satoshi Village
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 …| Satoshi Village
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 …| Satoshi Village
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 …| Satoshi Village
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 …| Satoshi Village
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 …| Satoshi Village
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 …| Satoshi Village
One network, with which many of my readers are familiar, is Facebook. At its core, Facebook is a network (graph) of users (nodes) connected by friendships (edges). Each user exists and experiences content within the confines of their Facebook subgraph, the portion of the network consisting of their friends. When analyzed properly, an individual’s friendship network paints a historical picture of his or her social engagement. Here I’ve created my Facebook friendship network …| Satoshi Village
Innovation in Medical Education Forum| blog.dhimmel.com
Dangerous dusts and malignant mesotheliomas: Q&A with Alison Grimes| blog.dhimmel.com
Electromagnetic pulses and slime molds| blog.dhimmel.com
My application to OpenCon 2015, the best conference ever| blog.dhimmel.com
The Cancer Research UK Reassessment of our Lung Cancer versus Elevation Study| blog.dhimmel.com
Elevation, Oxygen, and Cancer of the Lung| blog.dhimmel.com