jlafon
Joined 14 years ago
Karma
38
Submissions
39
Member since
Feb 18
Recent submissions
Comment · 5 years ago
Many have commented here on the computational challenges of enumerating, storing, and searching very large virtual libraries. While molecules can be represented and stored as strings, that's an oversimplification of the problem (from a CS perspective). Scientists often want to search these large libraries in 2D and 3D, which requires computing & storing those coordinates. It can be cost prohibitive just to store the 3D coordinates for massive virtual libraries, even for large pharmaceutical companies. We've done this for 10^10 molecules [0]. If you are reading this and find this type of problem interesting, checkout www.eyesopen.com/careers
[0] https://pubs.acs.org/doi/10.1021/acs.jcim.9b00779 "Virtual Screening in the Cloud: How Big Is Big Enough?"
Comment · 10 years ago
OpenEye Scientific | Santa Fe, NM | Onsite/Fulltime | http://www.eyesopen.com/careers
OpenEye Scientific Software provides software to the Pharmaceutical Industry for molecular modeling and cheminformatics. It has done so since 1997 in its continuing mission to provide novel software, new science and better business practices to the industry. Central to our approach is the importance of shape and electrostatics as primary variables of molecular description, platform-independent code for high-throughput 2D and 3D modeling, and a preference for the rigorous rather than the ad hoc.
We have three open positions in Santa Fe, NM. Some of the technologies we use are Python, Go, C++, Django, Docker, and AWS. We are growing our small team and looking for talented backend engineers and DevOps engineers.
Santa Fe is a beautiful mountain town with excellent outdoor recreation (hiking, skiing, cycling) as well as art, music & food culture.
Comment · 10 years ago
First of all, I'm not defending what is obviously predatory. However, there is more involved then what you might think at first glance. Right or wrong, correctional facilities have reasons to discourage phone calls (context: I put myself through college working at a maximum security prison). Calls are supposed to be monitored (usually done manually) to prevent criminal business from being done on prison phones - and there are never enough people to listen to all calls. There are never enough phones either, which frequently causes tension between inmates using phones and those waiting for them. In higher security levels phones are labor intensive. An officer has to escort a (potentially dangerous) person from their cell to the phone, and stand there for the duration of the call. And to the article's point, it's such a problem that prepaid phone cards are a form of currency on the inside.
Comment · 11 years ago
OpenEye Scientific Software (Santa Fe, New Mexico) - various positions: http://www.eyesopen.com/careers
Comment · 11 years ago
Nice work. I implemented something very similar last year: https://github.com/jlafon/pynamodb.
Comment · 12 years ago
That makes sense. I had only seen the Memcache & Redis datastores being used (and both being comparable to DynamoDB).
Comment · 12 years ago
It's interesting that Netflix decided to write this rather than using Amazon's own DynamoDB. I wonder specifically if DynamoDB was too expensive (as I have found), or was there some other reason?
Comment · 12 years ago
Author of the paper here. The file operations are distributed strictly without links, otherwise we could make no guarantees that work wouldn't be duplicated, or even that the algorithm would terminate. We were lucky in that because the parallel file system itself wasn't POSIX, so we didn't have to make our tools POSIX either.
Comment · 12 years ago
What I meant is that getting the toolbar to show up when you aren't serving from localhost isn't as trivial as setting DEBUG=True. It requires other settings (https://github.com/django-debug-toolbar/django-debug-toolbar...) which can be annoying to configure.
Comment · 12 years ago
I end up using Django Rest Framework (http://www.django-rest-framework.org/) generated UIs along with the debug toolbar, and then disabling the generated UIs when I'm done profiling.
Comment · 12 years ago
For those interested, here are a couple of differences between this and django-debug-toolbar (an excellent, widely used utility that also provides SQL inspection).
1. django-debug-toolbar can be difficult to enable if you aren't serving from localhost (for security reasons, because your settings are included in the UI). This project looks much simpler to enable, as you just set DEBUG=True in your settings.
2. django-debug-toolbar provides its information through a UI component embedded in your own UIs, but it doesn't help you with profiling HTTP APIs that don't have a UI. In contrast, this project puts some profiling information in the response headers, and SQL logs are sent to a logger. I think this use case is where Django Query Inspector shows a lot of utility.
Comment · 12 years ago
I'm trying to understand this too. This is only a problem if the OAuth provider (Google, Twitter, etc) does not validate the URL that the client is trying to redirect the user to after the user has authorized the app, correct?
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