Tag Archives: github

How someone uses GitHub and Zenodo to archive scholarly code

You can make GitHub repositories archival by using Zenodo or Figshare!
Wed 16 November 2016
By C. Titus Brown
In science.
tags: githubzenododoidatalib
Bioinformatics researchers are increasingly pointing reviewers and readers at their GitHub repositories in the Methods sections of their papers. Great! Making the scripts and source code for methods available via a public version control system is a vast improvement over the methods of yore (“e-mail me for the scripts” or “here’s a tarball that will go away in 6 months”).


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Filed under scholarly communication

August is Too-Many-Projects Month

(Tap… tap… tap… is this thing on? Good.)

July was vacation month, where I went on a glorious bike tour of the Oregon/California coast, and learned definitively that I don’t like biking on the side of a highway all day. Don’t worry, I escaped in Coos Bay and took trains and buses between Eugene, Santa Cruz, Berkeley, and SF for a vacation more my speed.

But now that I’m back, August is turning out to be project month. I have 3 great TCS applications to global health in the pipeline, and I have big plans to tell you about them soon. But one mixed blessing about these applications is that people actually want to see the results, like, yesterday! So first I have to deal with the results, and then I can write papers and blogs about the techniques.

Since Project Month is a little over-booked with projects, I’m going to have to triage one today. You’ve heard of the NetFlix Challenge, right? Well, github.com is running a smaller scale recommendation contest, and I was messing around with personal page rank, which seems like a fine approach for recommending code repositories to hackers. I haven’t got it working very well (best results, 15% of holdout set recovered), but I was having fun with it. Maybe someone else will take it up, let me know if you get it to work; networkx + data = good times.

    f = open('download/data.txt')
    for l in f:
        u_id, r_id = l.strip().split(':')
        G.add_edge(user(u_id), repo(r_id))

[get the code]


Filed under combinatorial optimization, software engineering, TCS