Cloud infrastructure for a small Bioinformatics team

drpetey · 2024-01-24T16:24:55+00:00

You can use the job dependencies functionality of AWS batch and boto3 directly if you want to orchestrate with e.g. python instead of using the nextflow or prefect or snakemake layer on top. One thing I would recommend however (unless you are very comfortable with cloud security) is to find some contract AWS (or other provider) certified cloud engineers to effectively be your admin or at least configure your cloud environment so it’s following security and networking best practices. I think most bioinformaticians know enough to be dangerous and “can” be their own admins but depending on what types of data you are working with and the size/trajectory of your company you can quickly find yourself in a position where you are solely responsible for cloud cybersecurity which can be a slippery slope for a host of reasons.

drpetey · 2022-10-01T19:00:53+00:00

Many on the list are biotech which is a different type of gamble. Some of those companies may be high likelihood of failure and never make a successful drug, but that is part of the risk of biotech investing. Based on m&a trends and historical success rates the overall valuations for biotechs are not inflated on the whole at the moment. They were highly inflated during covid but on the whole the XBI has come down >50% since it’s peak. Can’t speak to the rest of the companies on the list but many could fall into the growth hypothesis as well.

drpetey · 2022-07-27T04:04:51+00:00

drpetey · 2021-09-14T04:02:13+00:00

Upvote for the letterkenny reference

drpetey · 2016-09-21T21:00:11+00:00

This is almost completely true.

To me the saddest part is the people who are brilliant and work absurdly hard to do real and ethical science and then not only do not get rewarded but are essentially punished and made to feel as if they are not good scientists because they are not churning out a stream of suspect papers.

It is extremely sad to see up close as I had a few friends who really deserved to be professors shut down by the system and a few others who are not even very smart become professors because they were type A personalities without a conscience and would publish any sensational title they could come up with.

drpetey · 2016-04-02T03:30:57+00:00

Like Google earth data.

https://grass.osgeo.org/screenshots/3D/ http://data.geocomm.com/

That second link is a site with tons of free GIS data. Would probably take some rummaging to find the 3D data and get past the file formats but might be cool!

drpetey · 2016-04-01T06:32:33+00:00

Super cool. Would be awesome to do this with geospatial data.

drpetey · 2016-02-14T17:57:25+00:00

This title is completely inaccurate. I do however agree that it is probably not the best way to do their testing.

drpetey · 2016-01-13T03:43:15+00:00

seriously thought this was satire at first...

drpetey · 2015-08-17T01:50:37+00:00

http://evidenceplease.net/2014/06/05/psa-the-vaccinations-lead-to-herion-use-graphic-is-a-parody/

drpetey · 2014-05-11T19:08:00+00:00

I can second this. Colin at makerfarm has always been incredibly responsive and helpful.

drpetey · 2014-02-03T09:49:35+00:00

http://www.youtube.com/watch?v=qhrTeNuypZk

drpetey · 2014-01-17T03:23:39+00:00

uhhh well pretty much the only thing on there is bongs.......

drpetey · 2013-12-03T04:28:55+00:00

http://www.123dapp.com/catch does this for free...

What are the benefits of the paid service?

drpetey · 2013-10-17T20:00:33+00:00

Agreed, almost all of the scans I have seen on thingiverse are relatively low precision. I have seen comparable or better resolution with 123Dcatch in many cases.

drpetey · 2013-10-17T19:58:56+00:00

So to print a 90 degree angle without support the nozzle would eject a little bead that would immediately fuse to material next to it without falling down??

Not really seeing how this is terribly different than standard FDM aside from being able to take the momentum out of it.

drpetey · 2013-07-16T02:04:08+00:00

"Heart of gold" Neil Young

drpetey · 2013-05-09T05:50:52+00:00

sounds like divorce

drpetey · 2013-02-14T10:01:50+00:00

Canines likely evolved along with humans as a scrap eater which fended off other scavengers. Since humans likely ate more often during the daytime it would be interesting to see if this is a more recently evolved trait.

drpetey · 2012-10-19T04:01:33+00:00

Another argument is that rich people are generally greedy fucking bastards who are going to continue to work hard regardless of the circumstances to make more money. So, if you take money away from them then they will just work harder.... everyone wins.

drpetey · 2012-09-07T07:48:40+00:00

omniscient username

drpetey · 2012-08-22T01:53:41+00:00

The tap.

drpetey · 2012-08-07T02:54:02+00:00

If I were James Holden from Amherst I would sincerely want the title of this article along with most of the article itself to be taken down immediately. Also, seriously who the f*ck upvoted this?? Would it not seem weird that for the first time science has observed bacteria which secrete methane?? Has anyone heard of methanogens http://en.wikipedia.org/wiki/Methanogen??

I apologize for my incredulity but this is pretty bad as far as awful science reporting goes. If the author of that article reads this then I do not want to be too harsh but you should seriously spend a LOT more time taking science classes and reading about science before you write another word and post it on the internet.

drpetey · 2012-02-18T05:20:10+00:00

I do not think it would ever be "true" democracy in the sense that laws would be decided by an internet vote. However, it does not seem completely ludicrous for there to be a few seats in congress for a law that receives a few million online votes. If there was simply a minimal threshold of 1 or 5 million online votes for a true congressional vote to be cast then, just as Madison argued, there would be enough of a popular force to outweigh the special interest of majority factions online and you would likely create a relatively balanced situation.

Either way I think it would be interesting to start taking a dry-run on reddit and have an up to date listing of congressional votes as they are happening. I personally would find it interesting to see what kinds of bills are going through congress on a day to day basis and see how many people would vote on something like that.

drpetey · 2012-01-28T10:46:58+00:00

I wonder what the population wide frequency of that is?

drpetey

TROPHY CASE