New year reading roundup
This eye-opening post about relationships in academics...
...and the disproportionate pressure on women who hope to have children.
I doubt any selection committee would admit on-record to thinking a family-free candidate is “perfect”. Nonetheless, the traditional academic career structure is built around an assumption of mobility that is hard to maintain with any kind of relationships or dependents. I’m still trying to figure out if I can manage to keep a pet.
This thread on Hacker News about video-based MOOCs
I've participated in two MOOCs, but didn't complete either. I have mixed feelings about the use of video to present the material. In some cases, I could easily do without it. But in other cases I think it was helpful. Also, the types of autodidacts (many/most with a strong technical background already) that thrive in MOOCs may not need/want video as much as the average learner that would really benefit the most from a free or low-cost course.
As of 2016, I realised that video based courses in Coursera and Udemy are not ideal and are a drain on efficiency. You cannot skim through content in videos and you are constantly wondering what you will miss if you forward the video. You will have to adjust to lecturer's speed rather than choose your own speed. You cannot listen to videos in noisy environments.
This study on whether mom's kisses really do make owies feel better
BACKGROUND: The practice of maternal kissing of minor injuries of childhood (boo-boos), though widely endorsed and practised, has never been demonstrated to be of benefit to children.
OBJECTIVE: To determine the efficacy, if any, of maternal kissing of boo-boos in toddlers.
This piece from The Guardian about one case in which data sharing can be harmful
But earlier this year, an announcement in the Zootaxa academic journal that two new species of large gecko had been found in southern China contained a strange omission: the species’ whereabouts.
“Due to the popularity of this genus as novelty pets, and recurring cases of scientific descriptions driving herpetofauna to near-extinction by commercial collectors, we do not disclose the collecting localities of these restricted-range species in this publication,” the paper said.
This blog post on getting a faculty position
Now, I know what you are thinking – “Yuk, I don’t want a job at the University of Southwestern Northern Nunavut.” Neither do I, but here is the important thing to remember: You are not marrying your institution – you are dating it. If you don’t like it, you can leave – at any time and for any reason. The key is to get yourself into a job where you can prove your abilities as an independent researcher, get your start-up money, get a grant, do some teaching, and so on. That can happen at nearly any university in nearly any state or country.
This (paywalled?!?!) article about the NHGRI possibly terminating funding for several model organism databases
NHGRI Director Eric Green says that nothing has been decided and that rumors that his institute plans to phase out all of its funding are incorrect. But he and other NIH leaders are searching for ways to make the databases more efficient, and are urging databases to consider charging for use.
This latest BLAST+ release note from NCBI
With the upgrade from version 2.2.x to 2.3.x they have added provisional support for SAM output format.
This pre-print on amplification bias in RNA-seq
Need to read!
Computationally, read duplicates are defined via their mapping position, which does not distinguish PCR from natural duplicates that are bound to occur for highly transcribed RNAs. Hence, it is unclear how to treat duplicate reads and how important it is to reduce PCR amplification experimentally. Here, we generate and analyse RNA-Seq datasets that were prepared with three different protocols (Smart-Seq, TruSeq and UMI-seq).
This blog post on Netflix's new video compression strategy
The tl;dr of it all is simply that Netflix plans on scaling bitrates up and down based on the complexity of their video. So, slightly higher bitrates for busy action blockbusters and possibly lower bitrates for relatively static, flat cartoons.
Basically what we’ve all been doing for years with variable bitrate (VBR) encoding. But they’re trying to control that variance a lot more than an encoder like x264 typically allows. In fact, as near as I can tell, Netflix still plans on encoding everything with a constant bitrate (CBR), but they want to be really particular about the target number.
To do that, Netflix will transcode every one of their videos a bazillion times at different resolutions and at different bitrates, finally selecting the smallest one for a particular title that doesn’t suck visually. Seriously, their algorithm for all of this is quite clever.
This open-source OCR engine on GitHub
Found over Christmas break while chatting to family about OCR. By the way, it's available in Homebrew!