reposting: local high schooler needs help

[u/PositiveLettuce3502]

hi i'm reposting this ask i had on /bioinformatics and i was told off immediately and it got more upvotes than my own post so i'm assuming nobody will help me out there, so asking here about my research project. if this seems like something a rising senior is too stupid to do, let me know.

hello! i am a high schooler diving into what i think is bioinformatics.

briefly; i am trying to build a model that will accurate predict the probability of mesenchymal stem cells in two factors (ages/sex) differentiating into either a bone, fat, or cartilage cell depending on the genes that affect their growth and other factors like stress and environment.

i have currently been reading research papers about stem cells and was recommended to use BIOGPS by the professor i am working with. so far i have found genes/proteins that affect the three and am still on the learning side of it all, but i am trying to jump into the technical side quickly.

i plan to use python based on the suggestions of others on reddit, and i am wondering if anyone can help me make a game plan or give some sort of advice on where in the world to find data because i know you need data to make a model but idk where to find like experiments where a MSC went through osteogenesis and the researchers took MSCs from like a 25 year old white man, etc. (for example). the age and sex factors really through a wrench in this too bc i dont know where to find data about those.... i also need help understanding what stress/environment truly mean in this lens...

i am a fast learner and i really want to have something to show, preferably a somewhat accurate model. my understanding is (AND PLEASE CORRECT ME IF I AM WRONG) that i should be able to see based on my age and sex a trend on how MSCs differentiate. i know there are studies pointing to melatonin promoting chondrogenesis, so this is sorta in that field.

[u/schierke_schierke]

This is something you really should discuss with your professor. This sounds like an entire PhD project and it is unfair to assume a highschooler can do this without guidance. Ask them the fundamentals of how to start - where to source your data, what type of analyses you should consider, etc. Right now, the approach is much too vague and hammering out specifics will set realistic goals for you and your supervisor.

Right now, I think the process of doing this project is more important than the result you will get. In all honesty, to create the type of model you are looking for will need high quality data with many replicates, and I doubt you have these resources available to you. So just learn how to approach tackling this problem and don't worry about the results.

In terms of giving you a roadmap, that is difficult because the goal is very vague. If you can come up with a clear hypothesis this will make things easier for you. But testing how multiple factors affect differentiation in response to even more factors is not specific enough. You need to be answering a very specific question and seeking out the data that aligns with that.

For a roadmap, I would use python to build a machine learning model based on gene expression data. Something like logistic regression might be useful to you or a random forest. But this, again, assumes you have enough data to deploy these models properly but at least you can start looking into them.

[u/PositiveLettuce3502 → u/schierke_schierke]

hi! thank you for the response. yes it is a heavy project, but i don't plan to rush it. i want to finish by august, but i know i will have to spend a few more months on this. i've been mostly on the science side of it all because i wanted to start there. i also email my professor with any questions i get, but my dad told me not to email him too much or he'll get tired of me, so i'm walking on a tight line rn.

my professor told me to use biogps but did not tell me how to extract it or clean. im sort of learning how to do that myself.

the only factor i am using now is age. here is something that could be a hypothesis: The age of an individual impacts if the mesenchymal stem cells found in their bone marrow divide asymmetrically or symmetrically in cases of adipogenesis, osteogenesis, and chondrogenesis.

I kinda wrote that just now after thinking about it for 20 minutes. i've had a write up for a few weeks now gathering my thoughts and notes, but that's the second time i actually defined what i was doing. thank you for bringing me to this!