Another Word For It Patrick Durusau on Topic Maps and Semantic Diversity

February 1, 2017

Staying Current in Bioinformatics & Genomics: 2017 Edition

Filed under: Bioinformatics,Genomics — Patrick Durusau @ 8:31 pm

Staying Current in Bioinformatics & Genomics: 2017 Edition by Stephen Turner.

From the post:

A while back I wrote this post about how I stay current in bioinformatics & genomics. That was nearly five years ago. A lot has changed since then. A few links are dead. Some of the blogs or Twitter accounts I mentioned have shifted focus or haven’t been updated in years (guilty as charged). The way we consume media has evolved — Google thought they could kill off RSS (long live RSS!), there are many new literature alert services, preprints have really taken off in this field, and many more scientists are engaging via social media than before.

People still frequently ask me how I stay current and keep a finger on the pulse of the field. I’m not claiming to be able to do this well — that’s a near-impossible task for anyone. Five years later and I still run our bioinformatics core, and I’m still mostly focused on applied methodology and study design rather than any particular phenotype, model system, disease, or specific method. It helps me to know that transcript-level estimates improve gene-level inferences from RNA-seq data, and that there’s software to help me do this, but the details underlying kmer shredding vs pseudoalignment to a transcriptome de Bruijn graph aren’t as important to me as knowing that there’s a software implementation that’s well documented, actively supported, and performs well in fair benchmarks. As such, most of what I pay attention to is applied/methods-focused.

What follows is a scattershot, noncomprensive guide to the people, blogs, news outlets, journals, and aggregators that I lean on in an attempt to stay on top of things. I’ve inevitably omitted some key resources, so please don’t be offended if you don’t see your name/blog/Twitter/etc. listed here (drop a link in the comments!). Whatever I write here now will be out of date in no time, so I’ll try to write an update post every year instead of every five.
… (emphasis in original)

Pure gold as is always the case with Stephen’s posts.

Stephen spends an hour everyday scanning his list of resources.

Taking his list as a starting point, what capabilities would you build into a dashboard to facilitate that daily review?

Flattening the Earth: Two Thousand Years of Map Projections

Filed under: Cartography,Mapping,Maps — Patrick Durusau @ 5:08 pm

Flattening the Earth: Two Thousand Years of Map Projections by John P. Snyder. (Amazon link)

From the Amazon description:

As long as there have been maps, cartographers have grappled with the impossibility of portraying the earth in two dimensions. To solve this problem mapmakers have created hundreds of map projections, mathematical methods for drawing the round earth on a flat surface. Yet of the hundreds of existing projections, and the infinite number that are theoretically possible, none is perfectly accurate.

Flattening the Earth is the first detailed history of map projections since 1863. John P. Snyder discusses and illustrates the hundreds of known projections created from 500 B.C. to the present, emphasizing developments since the Renaissance and closing with a look at the variety of projections made possible by computers.

The book contains 170 illustrations, including outline maps from original sources and modern computerized reconstructions. Though the text is not mathematically based, a few equations are included to permit the more technical reader to plot some projections. Tables summarize the features of nearly two hundred different projections and list those used in nineteenth-and twentieth-century atlases.

“This book is unique and significant: a thorough, well-organized, and insightful history of map projections. Snyder is the world’s foremost authority on the subject and a significant innovator in his own right.”—Mark Monmonier, author of How to Lie with Maps and Mapping It Out: Expository Cartography for the Humanities and Social Sciences.

Perhaps not immediately useful for resistance but it isn’t healthy to remain in a state of rage all the time.

Delving into the history of cartography will help develop your understanding of and skills with map projections.

Government maps and projections represent the government’s hopes and wishes.

Shouldn’t you use projections that represent yours?

Challenging Anti-Whistleblowing Provision (Germany) [Republication of „stolen“ Data]

Filed under: Journalism,News,Reporting — Patrick Durusau @ 1:28 pm

GFF and its partners challenge anti-whistleblowing provision on handling „stolen“ data by Nora Markard.

From the post:

With an alliance of civil rights organizations and journalists, GFF is challenging the new Criminal Code provision on handling „stolen“ data. Passed by the grand coalition in 2015, this provision (s. 202d of the Criminal Code) criminalizes handling leaked data without providing for an adequate protection of the press. It thereby threatens an important part of the work of investigative journalists as well as their informants and supporting experts.

The facial challenge brought by GFF and its partners (PDF, in German) claims that the provision violates the freedom of the press and broadcasters, the equality clause, professional freedom and the clarity principle.

…

The new provision criminalizes handling data which someone else had obtained illegally; the sentence is up to three years in prison or a fine (translation by Sebastian Golla):

(1) Whoever procures for himself or for another, supplies another, disseminates or makes otherwise available data (s. 202a(2)) that is not publicly accessible and that another has acquired through an unlawful act, with the intent of enriching himself or another or of harming another, shall be liable to imprisonment not exceeding three years or a fine.

In the legislator’s intention, the provision addresses the trade in stolen credit card and user data. Due to careless drafting, however, it also covers the procurement, transfer and dissemination of electronic data which were obtained by journalists from whistleblowers.

Working with information such as that revealed to the public by Edward Snowden in violation of US secrecy laws would therefore be illegal under German law.
…

Governments are secretive creatures by nature and the German government is no exception to that rule.

Nora’s post is heavy on links to news coverage and those opposing this “accidental” sweeping up of whistleblowers.

Whatever the result under the particulars of German law, the better result would be a finding that publication, such as posting to Wikileaks or the dark web, breaks any chain of civil or criminal liability.

Once data has been posted to a public site, any re-publication of that data is protected as free speech.

It is easy enough to distinguish use of credit card data because that is a species of fraud and not an example of free (insert public) speech.

Re-publication creates a “bright-line,” one visible even to enthusiastic prosecutors and encourages leakers to leak for all and not the few.

Several recent leaks come to mind that were dribbled out for the benefit of the few.

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