ChaoticGenetics

@D32Palma @thebiologistisn Hahaha

Two fake follower accounts in the last few days. I wonder if I made it onto someone's list.

@thebiologistisn Nested polls? Very cool. Likey like.

Now, this is clunky as all heck and I don't expect it to be used well by respondents... but still, there is a way]

How to make a twitter poll with more than four options.

@thebiologistisn Hahah, yeah. Sometimes it's quicker to wait rather than go through the pain of parallallizing something. I usually use bash or python to break up work and run it in parts with MPI.

@ChaoticGenetics Scripted parameter scans is/are(?) exactly what I'm doing. Your cluster may be helpful. I'll need to think a little bit about the consequence of that architecture.

I was testing out Jellyfish (ver 2.2.6) on a random simulated genome and found some quirks. Running the program with 4 threads was much slower than 1 or 2. The computer was otherwise idle for all runs. Counter-len (used in structuring an internal hash) showed strong effects.

@thebiologistisn Yeah, yikes. Sounds like a cool 'how-do-I-deal-with-this-much-data' problem.

@ChaoticGenetics As of last June the species count was up near 4700. I expect it'll be above 5k the next time I run my scraper. I want to automate the construction of a phylogeny of those genome sequences. 5k^2 comparisons... so I want each step to take as little time as possible.

@thebiologistisn Cool! Can you script a 'parameter' scan? If you want to try it on my DIY cluster DM me and I will set up ssh access for you. The headnode is a dual socket Zeon server board with 24 GB.

@ChaoticGenetics Basically I want to find the fastest combination of settings for the range if genome sizes I'm working with (all published fungal genomes accessible via public databases), so I won't get a surprise 20 hour computation step.

@thebiologistisn Cool! What is limiting the speed? CPU/memory/IO? Also, could you 'parallelize' it further by splitting your genome into multiple chunks and running them concurrently?

As the "kmer length" gets larger, eventually most possible kmers are found at 0 or 1 times. For the largest kmers, I could thus use a single bit to keep track of their counts.

@sjohnson4888 @SeedSciSoc Maybe temp.? Bottom heat helps. Oddly enough, these seeds are germinating under far from ideal conditions - had to ask a lot of them for photography purposes.

@ChaoticGenetics @SeedSciSoc Ooo maybe I should try starting mine that way. I always have trouble getting them started even in the greenhouse

C. annuum germinating at ~30,000 fold speedup #seeds #timelapse #time-lapse #photography #video #ffmpeg #videoencoding #botany #biology #capsicum

@thebiologistisn Hahaha, yeah. Solid basic knowledge and some 'research' skill (google-fu) - interesting phenomenon. I consider it a good thing too.

The internet makes me look much smarter than I am in person with regards to identifying random plants. I'm ok with this condition.

@AgroBioDiverse @kctomato Woah, yeah. Surprised, sounds the the seeds at the World Veg. Center in Taiwan are dead and the Embrapa Clima Temperado is not able to provide seeds either.

@kctomato @ChaoticGenetics Wow, not much there genesys-pgr.org/explore?filter…

C. lanceolatum finally germinated! This one took almost a month. Not sure where these specific seeds are originally from but the species is native to Central America, spanning Oxaca/Veracruz Mexico to Honduras #biodiversity #capsicum #plants #peppers

@ClubLangholm @babyredpepperco

Wow one of our members chilli plants blooming like you wouldn’t believe :)

@AgroBioDiverse No, this one is official source unknown.

@ChaoticGenetics You have any sort of accession number for this?

@AgroBioDiverse @CGN_Wageningen Good catch! Sorry about that - typo, should be CGN20497.

@ChaoticGenetics Are you sure about that number? I can't find such an accession number in the @CGN_Wageningen #genebank database cgngenis.wur.nl/ToonResultaten…

Late addition! CGN2097 - Capsicum cardenasii: wild pubescens complex member from the Altiplano region in Bolivia. #biodiversity #peppers #capsicum #seeds #plants

@thebiologistisn Cool, hahah yeah, my problem exactly... Can't stop tinkering and/or germinating every seed I can get my hands on.

@ChaoticGenetics I'm hoping to do some paired trials this warm season. In the box vs. in the sun. I suppose I'd have to not tinker with the setup during the trial for it to perform informative...

I finally got my basement lab area sorted enough so I could build a lighbox around the plants I've been overwintering. The white surface of the plastic reflects back more light than the aluminum foil that is often used for this purpose.

@thebiologistisn Thanks for the shout out! One of these days I will get around to a good controlled experiment and measure the effect on generation time. Always seem to have too many varieties... Hard to block out time and space to grow a bunch of identical plants!

Though I don't have some of the technical aspects yet that are seen in other #SpeedBreeding projects (ex: twitter.com/ChaoticGenetic…), it probably doesn't take much to see benefits.

@b3roe @thebiologistisn Cool! Did you grow from seed?

@bhive01 Hahaha, IR to film continuous timelapse with constant light.

@ChaoticGenetics So, I was hundreds of nanometers off. I've had better days.

Can you guess the first upgrade to the #growthchamber? A bit superfluous, but I'm excited about it. #DIY

@bhive01 Close, other end of the spectrum...

@ChaoticGenetics UV LEDs?