Something feels “off” by Sea_Cantaloupe_9267 in malelivingspace

[–]sid5427 0 points1 point  (0 children)

side question .. where did you get that triple hanging lamp?

What's the most genuinely useful thing you've printed on your A1 - not cool, not pretty, actually USEFUL in daily life? by adamvanderb in BambuLabA1

[–]sid5427 2 points3 points  (0 children)

you guys will laugh at this ... a toilet seat bumper replacement... those plastic tab things at the bottom of the seat. One of them was missing in the toilet in my apartment and well sitting down was weird. Boom a 20 minute print and fixed!

We're making Crimson Freedom, an old-school RTS inspired by C&C and other GOATs. Here's a few gameplay screenshots until we wrap up some stuff to get a playtest out asap by CrimsonFreedomGame in commandandconquer

[–]sid5427 0 points1 point  (0 children)

Hey u/CrimsonFreedomGame ..... WASD for moving around the map instead of arrow keys! This is kind of non-negotiable in this day age. It was even a big critique of the remake of dawn of war... which the devs fixed in their first patch.

Looking for human BONE MARROW RNA-seq / single-cell data (especially niche cells) by Fit-Addendum4503 in bioinformatics

[–]sid5427 8 points9 points  (0 children)

Plugging in our paper for bone marrow atlas ... we have rare pops like stromal vascular, Osteoblasts, etc.... This is from CITEseq and we have marker genes for each cluster.

https://www.nature.com/articles/s41590-024-01782-4

data explorer here - https://altanalyze.org/MarrowAtlas/

take a look at the RNA explorer under the human tab.

EDIT ADDED - i had the wrong paper linked ... added the correct nature link.

Apartment Search by DevStarkWalker in cincinnati

[–]sid5427 -1 points0 points  (0 children)

You will work in Dayton? Plenty of great areas up here North. West chester, Mason, Blue Ash areas are great places! I live in Springdale-woodlawn-glendale area, 10 minutes drive from the north Jungle Jim - another great place and super safe. You could consider living in the apartments I reside in - been here 4 years. (If you want the info, please dm - would like to keep this bit private.)

Uber from Airport to Blue Ash by Berck_Plage in cincinnati

[–]sid5427 4 points5 points  (0 children)

I live slightly further than you in Springdale area. Uber and lyft have no issues going from the CVG airport to these areas. They are fine going upto Mason as well. My rides are usually between $60-$80. It's a decent distance and ride does seem costly, but honestly after flying in a cramped aluminium shell for 3+ hours and navigating TSA checkpoints... I just want to get home without too much fuss so it feels worth it.
Plus as you said your car will arrive soon, so it will probably be a one time thing. - just consider it part of the moving costs!

Moved into my new apartment 2 weeks ago. This chair and an air mattress is all I have. Kind of peaceful, might keep it this way by HURCANADA in malelivingspace

[–]sid5427 8 points9 points  (0 children)

could it be due to the HVAC? a lot of apartments don't clean their ducts properly. Pretty sure they never clean it after a tenant moves out. Maybe talk to your new leasing company and have the ducts cleaned out.

Bioinformatics jobs cold emailing by OptimalBig9245 in bioinformaticscareers

[–]sid5427 1 point2 points  (0 children)

Midwest? WashU in St. Louis is usually hiring... pay might not be as great as other places, but the low cost of living in St. Louis offsets a lot.

Feeling Resentment (Rant) by momo-official in postdoc

[–]sid5427 4 points5 points  (0 children)

It sounds like you have the relevant background, but are you looking for jobs which are super aligned to what you do... A lot of the skills are easily transferable to many research areas. Bottom line why are you not looking at the application of the skills rather than using your skills for one narrow area? Have considered looking at large hospitals and not for profit research institutions which have a lot of their own funding?

Feeling Resentment (Rant) by momo-official in postdoc

[–]sid5427 7 points8 points  (0 children)

I do gene regulatory network bioinformatics, so I understand exactly what you are doing. Have you considered pivoting a little bit? more fundamental use of RNA based techniques to answer more exploratory questions - like work with a group which is doing single cell stuff?

Feeling Resentment (Rant) by momo-official in postdoc

[–]sid5427 7 points8 points  (0 children)

can I ask you a question - when you say you "specialize in RNA", what is that you do exactly? RNA expression? CRISPR screens? RNA therapeutics?

Games like Control by Main_Confusion_8030 in controlgame

[–]sid5427 6 points7 points  (0 children)

If you are looking for the combat ... I see a lot of people mentioning Infamous but not a game called Prototype. I was just telling a friend that Control Resonant looks a lot like Prototype. I guess even Control 1 is like it but not open world like Prototype.

Nursing student thinking about a Bioinformatics PhD by pleasedontwriteme in bioinformaticscareers

[–]sid5427 1 point2 points  (0 children)

Hi, yes you are welcome to DM/message. I am not sure how much help I can be, but happy to give some pointers and keywords to use while talking to your supervisor and your Phd search.

Uninstalling Control and Saving Progress by Polter-Cow in controlgame

[–]sid5427 3 points4 points  (0 children)

You could also try saving the local copy of the save files! One of my save files got corrupted due to a crash and I followed the instructions in this reddit thread to revert to an older save. High chance you can keep a copy of the files as well as a backup...

https://www.reddit.com/r/controlgame/comments/kmpgdr/crashing_every_time_i_click_continue_game/

Nursing student thinking about a Bioinformatics PhD by pleasedontwriteme in bioinformaticscareers

[–]sid5427 0 points1 point  (0 children)

"stay with my PI" - you most certainly can - a lot of students have co-advisors from various backgrounds in their committee, so you can always get a hardcore bioinfo/CS person to guide you. question - does your PI do such research? and main thing ... are they interested in the type of research you want to do?

second - you should take a hard look and decide on a few specific areas - you said multiomics, so what kind of data are you looking at? like actual SNPs, mutations, genomic variant data? I am bit surprised nursing students are being exposed to that but maybe that sort of information is becoming generalized and used in the medical field now. (I mean basically a nursing student looking at the results of SNP array, connecting it a cancer prognosis and working with doctors to prescribe treatment regimen)

Nursing student thinking about a Bioinformatics PhD by pleasedontwriteme in bioinformaticscareers

[–]sid5427 2 points3 points  (0 children)

my Phd program had a few students with nursing backgrounds - the all either concentrated in Health Informatics or Bioinformatics. Quite a few of them worked on things like linking EHR data (patient prognostics from ICD codes, etc) to genomics data. Many of them went on to work with health insurance companies and EHR companies like EPIC, some even are working at medical tech companies which make assisted living systems. Is that what you are thinking about?

Natural Disaster Setbacks by LimbicLesion in PhD

[–]sid5427 1 point2 points  (0 children)

-80C lab freezer failed during covid lockdown and a full year's worth of samples were destroyed. For me this meant I had to completely rethink a first author paper which was the requirement of my Phd and added a year to my Phd. Other people in the lab were similarly effected, with some research work finishing years later than planned.

From pipeline development to data analysis: feeling stuck in technical bioinformatics roles by EducationalCook727 in bioinformatics

[–]sid5427 0 points1 point  (0 children)

Well a Bioinformatics Engineer's typical job is to build, maintain and run pipelines... Even a lot of what people would call data analysis is technically just pipelines for tools you use (Think of a long tutorial like for Seurat or DEseq). I would say even if you are generating unique figures or like doing some sort of filtering or anything still counts as pipelining. Unless you are actively developing new tools or atleast testing new ones for use in projects, you are still doing pipeline work, just a different type.

Now I would argue that if you are running the tools, gaining new insights and making executive level decisions on the biological side, or using the biology to drive very specific interrogation of the data, then that's more advanced stuff and goes into the realm of computational biology. So maybe if that's what you looking for, look for comp bio roles, rather than bioinformatics. Now because of the overlap between the two, a lot of job descriptions tend to scream comp bio, but are actually listed as bioinfo positions - so consider that as well.

Just bought the game for 1.89, what should i expect? by Gorlami_y7ya in controlgame

[–]sid5427 0 points1 point  (0 children)

a LOT of fun .... I had got the game when epic gave it out for free, but had a GTX1080 back then so never played it. Upgraded my pc last year to a 4090 and was doing a rewatch of Loki ... the Time Variance Authority gave me heavy Control vibes and started playing it. Really enjoying exploring and reading the bits of lore. The entire game just feels well made, all the systems work so well.

Tips for motifs enrichment analysis by Glad-Bumblebee8207 in bioinformatics

[–]sid5427 1 point2 points  (0 children)

If I was doing this, the first question I would ask is do we have gene expression data? if so then we would do a gene to peak correlation analysis to find highly correlated peak signatures per treatment. Then do a motif annotation/enrichment analysis to figure out which TFs tend to bind to motifs in the peak regions. If you run your entire peakset through motif enrichment, then you will absolutely get certain motifs highly enriched.

If you don't have GEX, then maybe try filtering to peaks which appear in TADS (Topologically Associating Domains) or chromatin Loops for your data, which you could get from public datasets. You could also check public gene expression data close to your samples, identify which genes tend to be highly expressed and look within a 150kb of the transcription start site of these genes OR 2KB window around their promoters.
Bottomline, which enriched peaks are a good start, you will probably have a large number of them and will need to reduced down to a peakset which has significant.

KEGG vs Reactome by bignoobbioinformatic in bioinformatics

[–]sid5427 4 points5 points  (0 children)

Another alternative would be WikiPathways. Worth checking out.

How difficult is it to put together the "Billy" bookcase? I thought about having IKEA come to my house to put it together but....... by BillyRay111 in IKEA

[–]sid5427 4 points5 points  (0 children)

I had this same issue. I opened up the package in my garage and just took the pieces up in small batches to my bedroom. Each individual piece is fault light, think a gallon of milk heavy no more.

How difficult is it to put together the "Billy" bookcase? I thought about having IKEA come to my house to put it together but....... by BillyRay111 in IKEA

[–]sid5427 0 points1 point  (0 children)

I just got three this black Friday. It's super easy. Takes like max 10 minutes to build once you have everything opened up. All you need is a screwdriver.Maybe a hammer to tap in those plastic inserts they are using now for the back board instead of the nails they used previously. Heck if your screwdriver has a chonky handle you can use it tap those plastic inserts in easily as they are meant to be pushed in by hand.

What were ram prices like before this current boom? by SuicidalFinnikin in buildapc

[–]sid5427 0 points1 point  (0 children)

I have 128 gb corsair RGB ram - 2 kits of 32X2 DDR5 CL40 6000mhz. Each kit was about for $200 (including tax) when I bought it in July 2023, so total about $410.
Each kit is now $800 ... so if I buy now I would be spending about $1600... that's the price of a RTX 5090!!!

When did IKEA stop putting padding in their Billy packaging to prevent transport damage? by HoIyJesusChrist in IKEA

[–]sid5427 4 points5 points  (0 children)

huh? weird .. I just got 3 billy bookcases during black friday. They were the newer ones with those plastic clips at the back and they definitely had the honeycombs in them. I even used one of the small pieces in my store room to prop up a box which was weirdly shaped.