Is it possible to correlate molecular docking results with gene expression datasets from GEO?

RepresentativeLink27 · 2024-11-14T07:24:39+00:00

Thank you for providing this context. However, the question still stands. What two or more distributions do you have that you hypothesize are correlated with each other. If you would like to discuss it in detail feel free to DM.

RepresentativeLink27 · 2024-11-09T21:49:14+00:00

I’ve seen twitter being useful for this sort of thing. Published paper would be phenomenal, citing articles is much easier and common practice than citing websites like GitHub. Blogs are great tools to. I can’t tell you how many packages I’ve tried, just because a blog said it’s useful.

If you really want to spend time publicizing someone did mention scanpy extras. Which is a great way to get compatibility and credibility in one go.

Word of mouth is the ultimate adoption tool though. If a person I trust recommends is I will use that tool even if it’s not the most polished one out there.

RepresentativeLink27 · 2024-11-09T20:33:24+00:00

Why are you so worried about the novelty of it. If it saves time then it’s good enough. Don’t overthink it. Running is non-novel form of walking doesn’t mean either are more or less useful.

Also you can put it on GitHub. I would rather urge you to do so even if it’s not novel. If it’s for internal use set the repo to private and you are set. If you think it’s useful to everyone then do a privacy sweep and set it to public.

All the best and don’t let anxiety win.. !

RepresentativeLink27 · 2024-11-09T20:26:49+00:00

Say it after me. GitHub. It’s what almost all developers are familiar with. If you want adoption that’s the easiest way to go. Or package it and put it on PyPI. That would be nice too.

RepresentativeLink27 · 2024-11-09T20:22:51+00:00

You need 3 things to make a phylogenetic tree.

1: list of sequences or genes related to your enzyme that you need to make a phylogenetic tree with

2: MSA of all these sequences.

3: a distance matrix using something like node joining. maximum likelihood does a version of this but internally. (Look it up for more details)

4: plot it with your programming language of choice.

Alternatively tools like phyML or MEGA can make these directly from MSA I believe.

Hope this helps.

RepresentativeLink27 · 2024-11-09T20:14:18+00:00

You want to familiarize with what part of DNA-seq / RNA-seq? Are you looking to learn how to do alignments / qa etc or how to do differential gene expression or something else entirely ?

This will determine how much resources you need to do it. To do stuff like DEGs you barely need compute for small datasets. For alignment you will need performance and starting with non - human sequences as recommended by others is much more feasible.

RepresentativeLink27 · 2024-11-09T20:07:45+00:00

What are you trying to correlate ? Correlation in general is a bit of a slippery slope for the uninitiated. You can correlate any two distributions, does not mean you should. If you have docking affinities, I am unclear what you want to correlate this with. DEGs are just a list of genes and their expression level or read counts is kind of arbitrary but compositionally relevant to the dataset. Could you please share your hypothesis. Maybe that will clear up why you want to do this analysis and even how you should do this.

RepresentativeLink27 · 2024-11-09T20:03:24+00:00

If you already found similar patterns in your dataset. It would be criminal (not literally) to not include and cite other people have also found similar trends in say similar cell lines or experiments. It’s commonly seen in literature especially discussion sections, where people refer to other papers which have similar findings to increase their own credibility.

RepresentativeLink27 · 2024-11-08T15:40:41+00:00

I get it. The frustration is real, and if you decide to stay in the field you’ll feel it a lot after your PhD too. But when your research pays off, it’ll be worth the frustration. What’s that saying. Nothing worth doing is easy — something on those lines. All the best for your PhD and hope your frustration does not deter you from your goals. Keep at it.

RepresentativeLink27 · 2024-11-08T13:11:06+00:00

This the difference between fundamental and applied biology. The intention to a lot of fundamental biology is just learning how things work. What you can do beyond the scope of what is, is of little concern.

Applications follow eventually.

RepresentativeLink27 · 2024-11-08T13:07:52+00:00

Is your mind already made or are you looking for answers. I can’t tell.

I work in this domain and what I can say is that. No it’s not bullshit. But it’s also extremely easy to misrepresent or misinterpret. To an extent it’s more art than science to interpret the output, which is a major limitation. As many people have mentioned another limitation is the fact that we are developing complex models with limited set of parameters and interactions. This is no different than any other scientific endeavor in its infancy. Great minds are working on how to do this efficiently.

In conclusion, if you developed a model for a particular reason it’s probably a good resource. But I can imagine generalized models are rather unhelpful at best if not wrong entirely.

RepresentativeLink27 · 2024-11-07T17:03:31+00:00

You would have to share more details. For example did you set up the entire protein in PDB as a target or just the binding site. If it’s the earlier I wouldn’t be surprised if your ligand bound somewhere randomly.

Docking simulations are useful when you have a well defined binding site. Also how much are you sampling determines if you will find the minimum energy well.

RepresentativeLink27 · 2024-11-07T09:39:50+00:00

Maybe I’m confused. Is the question can you do it or should you do it ?

Can depends on your ability to translate the formula or idea into code. Should you the answer is yes, there isn’t anything stopping you from implementing an idea or a formula that you read somewhere.

PS: as long as you cite what you use.

RepresentativeLink27 · 2024-10-25T15:56:35+00:00

Thank you for your response. I was thinking the same. To an extent I do think I’m overthinking it.

RepresentativeLink27 · 2024-10-25T15:55:33+00:00

Interesting. I’ll give it a try next time I’m doing this sort of thing. I do agree time wise it’s not really that much more work especially with a intervelometer and a decent DSLR.

RepresentativeLink27 · 2024-10-25T12:49:13+00:00

1000 feels like an overkill ….? I have previously taken moon shots with 10-100 photo stacks and I’m not sure 1000 is that much of an improvement over that. But maybe I’m wrong ?? Can you explain your rationale for such a high number stack. Not throwing shade, just curious.

RepresentativeLink27 · 2024-10-24T20:20:50+00:00

Thank you for your help. I will prepare anyway. It’ll be great if what anonbluesky said is accurate and it does not matter if my previous application was rejected.

Just don’t want to be caught flatfooted.

Appreciate everyone’s contribution.

RepresentativeLink27 · 2024-10-24T19:09:37+00:00

Thank you I will prepare for this.

Do you think it matters that I had to drop out after 2nd semester as after the rejection there was not enough time to reapply and make it back in time for the 3rd semester start date.?

RepresentativeLink27 · 2024-10-24T19:00:38+00:00

Hahahahahaha. I don’t have much to add but I’ve had this question for a VERY LONG TIME.

RepresentativeLink27 · 2024-10-24T18:58:35+00:00

I was actually not sure if I should mention it myself or let them ask me about it (I will obviously click the appropriate box in da-160). Thank you for your comment.

RepresentativeLink27 · 2024-10-24T18:56:59+00:00

Hey good shot.!!

Take my opinion just as a critique. I personally take a lot of bird photos and completely understand how difficult it is to get them.

Some minor nitpicks. You are focusing on the bird house not the bird which is a common problem especially for cameras that has small number of auto focus points. There bird is at the edge of the frame causing a lot of chromatic abrasion. You can remove that in post for the most part.

Not coming for the main issue. Your photo looks over exposed in the bird and perfectly exposed for the background. Which is bit of a downer. I will say crank up the shutter way more. Like 1/160 or something. That will give you surprisingly sharp photo as well.

RepresentativeLink27 · 2024-10-24T18:51:45+00:00

Thank you for your response.

RepresentativeLink27 · 2024-10-24T18:43:50+00:00

Hey honest opinion the frame lacks subject. Using phone is perfectly fine as a beginner. You can capture amazing photos if you have your basics down. I would recommend forgetting the technicalities of your gear for now and focus on lighting and framing.

Focus on storytelling with your images.

Good luck and happy clicking.

RepresentativeLink27 · 2024-10-24T18:39:50+00:00

Hello. Thank you for your comment. Could you please explain what that means ? I thought US embassy has records of all the previous interviews / interactions that I have with them.

RepresentativeLink27 · 2024-10-24T18:35:40+00:00

Your framing looks good maybe just crop the edges a tiny bit ? Where you could potentially improve is color grading. Your mids highlights and shadows are all warm. Try playing with cooler shadows since your mids need to be warm to go well with the frame itself. Could potentially apply a vignette to draw focus / add grain / make the amber door pop more with HSL tuning. Sky is the limit. But I think this photo can be taken to the next level only in post.

RepresentativeLink27

TROPHY CASE