Hi, I will soon be starting a PhD and I need a new laptop. Does anyone have a recommendation on which laptops are best to work with software related to Cognitive Neuroscience (EEG, MEG etc but also neural networks) and genomics (analysis of RNA-seq, transcriptome, single cell etc)?

I am used to Mac but I feel like they're not the best for software :(

I recently did a GeneSight test and would like to know what this means. SSRIs don't work too well for me and I'm having a hard time finding something to help my depression. I also have reduced folic acid intake. Any suggestions or help would be greatly appreciated!

US startup charging couples to ‘screen embryos for IQ’ https://www.theguardian.com/science/2024/oct/18/us-startup-charging-couples-to-screen-embryos-for-iq?CMP=share_btn_url

Are they screening the embryo for intelligence, or the parents' intelligence?

What is the best way to get your whole genome accurately sequenced? Is there a particular provider that offers top tier sequencing? Is it best to take your raw code and utilize an online tool for DNA evaluation? If you could give me the best methods, it would be greatly appreciated! (Also I have a doctor willing to prescribe tests codes/tests too)

I want to get one insect genome sequenced to at least draft level. Our institute does not have any staff with a Biotech, Bioinformatics, or Molecular Biology background, and I myself am a biochemist. I have only sequenced a few genes using Sanger's method. In my circle, people have gone for Nucleome, Neuberg, or Eurofins. It would be of great help if someone here could provide me with some names with whom they had good experience.

Hello r/genomics!

I will be honest, I'm not sure if this is the right place to post, apologies if misguided. It didn't seem to break any of the rules, so fingers crossed!

For those of you that work on bacterial pathogens and regularly calculate SNP distances between isolates, I was hoping to find some folks to take my new Nextflow pipeline CSP2 out for a spin.

CSP2 is the next iteration of the CFSAN SNP Pipeline, and can infer SNP distances between bacterial monocultures using genome assembly data (i.e., no WGS read data or read mapping required). Comparisons of hundreds of isolates can be performed using multiple references, with runs completing in minutes versus hours.

My internal testing has been encouraging, but you never know how something will fare in the world until people use it. In that sense, I wanted to throw a little invitation out to anyone that might be interested in speeding up their analyses. Happy to answer any questions for folks here!

https://preview.redd.it/tw48rnnlmdvd1.png?width=416&format=png&auto=webp&s=cb29897ee5b3c45a20cd9854949393184782b0ec

https://github.com/CFSAN-Biostatistics/CSP2/tree/main

I’m presenting an article for my University’s genomics group soon and want to find an incredible paper. What’s the best genomics paper you’ve ever read?

Human DNA is 3.2B base pairs, each pair can be encoded in 2 bits, which means 6.4B bits = 800 MB.

If I compressed this 800 MB file using a standard algorithm like zip and bzip2, what would be the compression factor?

Hello, I created a simple website that helps students interested in specific biomedical topics find labs that would be the best match for them. You can check it here: https://pi-match.web.app/

The website queries the free and open PubMed API to identify last authors who have published the most papers relevant to a student's interests.

Let me know if you would like more features.

I did whole genome sequencing through nebula awhile back and have no clue what to now do with the data? Any suggestions?

Hey everyone, I am currently heading into senior year of college and am majoring in biostatistics. I wasn’t sure what I wanted to do with that but someone recommended genomics and it really got me interested. I know some python and r, and am looking into grad schools, but I was wondering if you guys have any advice for getting involved in genomics? Thanks!!

Can anyone explain what the differences between the 3?

Hi. I have a PhD in biochemistry and work as a software engineer, so I'm kind of familiar with the science and technology involved here, but not an expert in either. I know there are some commercial offerings for cats and dogs, but I'm thinking of less popular pets, like rats, and maybe some other critters. Can someone verify my guesses of how it could work? This is an early idea phase, so please don't send me job applications, yet:) Help me figure out whether it's doable (economically) first. Basically, I'm trying to find out what pieces are already there. I don't want to start with building lab for tens of thousands of pounds/dollars/euros if we can get better results and cheaper by sending samples to people who know what they are doing. In the first phase at least, until we have useful data and customer base. Or if it turns out there is no demand, then I won't have to sell the lab :P

Step 1 - Whole Genome Sequencing and identification of SNPs.

There are complete genomes available for many species already, including rats. But for rats specifically they only sequences lab rats, who are heavily inbred, so their SNPs are probably useless for pet rats. I guess I would have to sequence a dozen or so pet rats with diverse range of coats and other traits of interest, and identify the more relevant SNPs myself. As this is only required during the setup phase, I would probably outsource it to existing WGS companies. What would be the cost of such operation, given that rat's genome is similar size to human?

Step 2 - Micro-array testing for common traits.

This is a basic service, at least until we have enough SNPs identified for diseases and such. I could either learn to do it myself (more likely hire an intern), or again, find some commercial provider. What are the commercial options here? Are there companies which will prepare and run micro-arrays based on the list of genes I give them? At what cost?

Step 3 - Ancestry.

This would probably happen in the same phase as step 2, but I list it separately, because rats don't have registered breeds or pedigrees, so it's optional, with probably little demand for this. I believe this could be done by "simply" comparing number of shared SNPs, but it's usually done in a bit more advanced way, by comparing lengths of shared segments. In either case, it's the same kind of micro-array testing as traits, but slightly different comparison algorithm.

Step 4 - Finding new SNPs.

The first set of SNPs identified through sequencing the initial sample population will not be sufficient for long. Companies like 23andme continuously add more SNPs by asking the patients to fill surveys and analyze their answers and genomes together. But how do we find these new SNPs if they were not present in the initial sample? Do we need to do WGS each time we get a pet with new traits, or do unknown SNPs sometimes "show up" in micro-array testing, by maybe the match being a bit off, or something?

Could an adult be changed in their genomics?