Jeremy Jay

@thepbnjay

Thoughts on tech, bioinformatics, data science, big data, and father of 2. Research Asst. Professor . Obviously my thoughts are my own.

Charlotte, NC
Vrijeme pridruživanja: prosinac 2009.

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  1. Prikvačeni tweet
    31. sij
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  2. proslijedio/la je Tweet

    How support reproducibility will be a discussion topic at our upcoming workshop on 2/11-2/12. This topic will feature /, Travis Richardson/, and Nici Pfeiffer/. Register:

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  3. prije 5 sati

    This will forever sum up San Francisco versus the Midwest

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  4. proslijedio/la je Tweet
    prije 16 sati

    .....”and that, grandchildren, is how the state of Missouri ceased to exist when it was forcibly nationalized and ceded to Kansas.”

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  5. proslijedio/la je Tweet
    29. sij

    Posted without comment

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  6. 31. sij
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  7. 31. sij

    It's running! (sorta) Seems like a good place to stop for the day. In the next installment we'll actually try to get some data loaded in...

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  8. 31. sij

    Luckily, documentation saves the day again: when I added sessions.php I included the source URL at the top: within the comments is a table schema!

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  9. 31. sij

    There's a file named "ode_schema.sql" in the filesystem root... could it be that easy? Other than a few errors trying to lock down permissions (we can safely ignore those for now), it went without a hitch! However, it looks like we didn't include a session storage table...

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  10. 31. sij

    Instead of dealing with container linking... we'll just install postgres inside the same container with php. I did the default postgresql that came with jessie, 9.4.25, since I know that there weren't any major backwards-compatibility issues going from 8 to 9.

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  11. 31. sij

    This was a fun bug to track down... sometime in the php5 era, the default for so-called "short open tags" switched from "on" to "off" in php.ini. Essentially, if you have code that starts with "<?" instead of "<?php" then it won't even execute. Handy! Now for the missing DB...

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  12. 31. sij

    I'll spare you the details, but let's just say the official php5 docker images make it impossible to add the pgsql extension... So I went back to a debian jessie container and started from scratch. Success! (well... no more missing extensions at least)

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  13. 31. sij

    It looks like the oldest "official" version of php we can get on docker is 5.4, but there's a tag that even include apache! I see the old favicon! but alas there doesn't seem to be postgres support. That would have been too easy

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  14. 31. sij

    OK What software do I need to dig up... luckily, we did include some of the version information in the manuscript. I like to think we did insulate fairly well, it's still going today!

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  15. 31. sij

    Based on commit messages, it looks like June 3rd I had started a transition to smarty templates. It looks like this took about a week of refactoring, doing a page at a time... so I think it will be safe to start with the codebase just before that: 07c249f on June 2nd

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  16. 31. sij

    In 2009 I was still a graduate student, and we were using SVN for version control. We wouldn't switch to git until another year later. First lucky break though: I was such a pendant (ok, still am...) that I preserved all the svn history during the switch to git.

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  17. 31. sij

    Just to give myself a date, I'm going to use the date we submitted the manuscript: June 3rd, 2009 We used a lot of different data sets for the first analysis, I wonder how many have archives that far back?

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  18. 31. sij

    Let's see how far down the rabbit hole we can get! We published the first real manuscript for the Ontological Discovery Environment in 2009: So it fits the 10 year challenge pretty closely, and I still have access to the code!

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  19. 31. sij

    Just finished so I'll be done with philosophy for a few bearimys now.

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  20. proslijedio/la je Tweet
    30. sij

    Keep the alive and attend the Metadata Automation DREAM Challenge webinar today at 12 p.m. ET. Drs. and Thomas Schaffter will lead a panel session with challenge organizers. Tune in:

    Metadata Automation DREAM Challenge. Partners include: Cancer Systems Biology Consortium, NCI Cancer Moonshot (A program of the National Cancer Institute of the National Institutes of Health), National Center for Data to Health, Physical Sciences in Oncology, Sage Bionetworks.
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