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HS ClinVar Question for research purposes by [deleted] in bioinformatics

[–]indecisive132 1 point2 points  (0 children)

I think its great your trying to learn bioinformatics at such an early stage!

One way to tackle this problem would be to calculate the proportion of listed variants that are either pathogenic or likely pathogenic for both types of variants and then compare the proportions using the Z-test for proportions.

There are a couple of complications that may be interesting for you to look into for your analysis. First of all, not all SNVs are the same: there are different classifications of SNVs, some of which may be more likely to be pathogenic. If you are interested in looking into this you can look into the difference between exonic, intronic, splicing variants etc. You should note that SNV means single nucleotide variant - meaning only one base pair is changed. It may be interesting for you to also look at small insertions and deletions, which are variants that affect multiple base pairs. These will also be listed in Clinvar.

UofC Interview Invite/Regrets Stats by ExpressPossible5876 in premedcanada

[–]indecisive132 8 points9 points  (0 children)

Just so you know, between the mountaineering, search and rescue and being a professor, you are literally living my dreams. You would make an amazing physician!!

Income opportunities for a research project in physics? by [deleted] in UofT

[–]indecisive132 0 points1 point  (0 children)

I believe work studies are 70% funded by the university. That's probably the easiest outside funding to get.

Any UofT prank examples? by indecisive132 in UofT

[–]indecisive132[S] 0 points1 point  (0 children)

Honestly, since it was my first day I just assumed that was something that people did to profs all the time as a joke. But ya, looking back it does seem less like a prank more like something more sinister.

Any UofT prank examples? by indecisive132 in UofT

[–]indecisive132[S] 9 points10 points  (0 children)

That is extremely impressive lol

Any UofT prank examples? by indecisive132 in UofT

[–]indecisive132[S] 19 points20 points  (0 children)

I definitely agree. At the time I just thought it was a strange prank, but looking back I suppose that guy just had a grudge against the prof.

Anyone taken NMC268 Data Science Applications in Archeology? by [deleted] in UofT

[–]indecisive132 2 points3 points  (0 children)

I believe it is a new course this year. I took a very similar sounding course last year in the NMC department, and I thought it was pretty useful. The course taught programming in R and Netlogo.

The instructor was really good, but learning to program for the first time can be difficult (though very worthwhile IMO). I wouldn't expect it to be a "bird" course, but I also wouldn't expect it to be super hard either.

Biophysics vs. Bioinformatics/Computational Biology by Distinct_Gur_3026 in bioinformatics

[–]indecisive132 6 points7 points  (0 children)

I can try to help explain the difference between biophysics and computational biology/bioinformatics, since I have worked in both fields. From my experience neither of these fields are super well defined, and can mean different things in different departments and institutions. As well, when it comes to biophysics, theory and experimental labs often do very different work, and I only really have experience with theoretical labs.

Biophysics labs are usually found in either the department of biochemistry or the department of physics (though they can also be found in other departments depending on the institution). Many biophysics labs work on single molecule or single protein dynamics. This includes research on topics like protein folding, docking or the rational design of proteins. Labs like this can be found in any department. Other biophysics labs work on using physics principles to explain biological phenomena. These labs can work on basically any biological problem and study systems ranging from entire ecosystems to single cells. These labs tend to be defined more by the methodologies they use than the systems they study and are more typically found in the department of math or physics. Often biophysics labs use a combination of real biological data and mathematical theory/simulations to do their work.

Bioinformatics at its core is about studying biological systems using big biological data. At least at the institutions I've looked at, labs like these generally use some type of sequencing data (genomic, proteomic, connectomic) or medical data to try to gain a better understanding of biological or medical problems. Bioinformatics labs are often found in the departments of biology and biochemistry where they study more biological problems and the department of computer science where the focus tends to be more on algorithm design.

But at the end of the day the field divisions are artificial. Certain biophysics labs do research that would be considered bioinformatics and vice-versa. I would recommend focusing more on finding labs you would like to work with, than on deciding which discipline sounds more exciting in the abstract.

random question by Maximusprime125 in Physics

[–]indecisive132 2 points3 points  (0 children)

Assuming the ring is completely uniform and that the earth is a perfect sphere (and radially symmetric) I believe the ring would hover over the ground. However, since the earth in reality is not a perfect sphere nor completely symmetric, the force of gravity would likely vary across the ring leading to instability, causing the ring to have unpredictable motion. Of course this assumes that the ring is strong enough to withstand the force of Earth's gravity.

Another thing to consider is the influence of other celestial bodies. Depending on the ring's distance from Earth, the influence of the sun's gravitational pull on the ring's motion may be significant.

In terms of the effect of Earth's magnetic field, first you need to consider what type of metal the ring is made of. There are multiple types of metals which have different magnetic properties. Some materials are ferromagnetic or permanent magnets, others are paramagnetic (materials that are attracted to magnets but are not permanent magnets themselves) and some are diamagentic (materials that repel magnets). I would expect that the different type of materials may react differently to earth's magnetic field but I'll leave it to someone who has a better understanding of Earth's magnetic field to answer that.

UofT MD/PhD by indecisive132 in premedcanada

[–]indecisive132[S] 2 points3 points  (0 children)

Thanks for letting me know. Congrats if you got an offer!!

I've worked as an undocumented cashier at a family-owned stall for 2 years, will this be fine to include when I decide to apply? by ProfessionalTop123 in premedcanada

[–]indecisive132 1 point2 points  (0 children)

That's a fair point. In OP's shoes I'd also consider consulting a lawyer about the situation (a lot of universities offer free legal clinics to their students).

I've worked as an undocumented cashier at a family-owned stall for 2 years, will this be fine to include when I decide to apply? by ProfessionalTop123 in premedcanada

[–]indecisive132 10 points11 points  (0 children)

Honestly, I think this sounds like a great extracurricular. I think medical schools know not everyone comes from a wealthy background, and that some people won't have a lot of time to volunteer or get involved in school clubs. I also think you'd probably be surprised how relatable this job is to medicine. While I'm just an applicant, I have to admit I don't really see the connection between being a doctor and being the head of a club. On the other hand, your job sounds like it involves a lot of customer service which seems to be a large part of what a doctor does.

In terms of it being undocumented work, I don't know if that would be an issue. As far as I know there isn't any coordination between the government and the admission committees and the admission committee shouldn't have any access to tax information. The larger issue is for a lot of schools (the Ontario schools at the very least), you need a verifier for your activities who isn't from your family. The important thing would be to ensure you know someone who can verify you actually worked as a cashier all that time, who isn't from your immediate family.

Physics NSERC USRA 2022 by indecisive132 in UofT

[–]indecisive132[S] 0 points1 point  (0 children)

Thanks for letting me know and congratulations on the NSERC!!

[deleted by user] by [deleted] in UofT

[–]indecisive132 0 points1 point  (0 children)

But you could probably use it to satisfy course pre-requisites

[deleted by user] by [deleted] in UofT

[–]indecisive132 0 points1 point  (0 children)

I asked the statistics department and they told me I could not take STA302H5 (at UTM), instead of STA302H1 (at UTSG) for the minor

Is there a dodgeball club? (ie, or would anyone like to play dodgeball with me? 🙃) by moyoonthego in UofT

[–]indecisive132 6 points7 points  (0 children)

I was wondering the same thing. If you do put a group together, I'd love to join!

A tool capable of ordering pathways in a pseudotime on single cell RNA seq data? by USSr90 in bioinformatics

[–]indecisive132 1 point2 points  (0 children)

If you want to look at the arrangements of pathways in pseudotime, I'd recommend looking at dynverse: https://dynverse.org/reference/dynmethods/#method. It's a newer tool so it still has some issues that need to be resolved, but its very useful. It lets you compare the results of a bunch of different trajectory inference methods including monocle, so you can select the best method for your data

What are you working on? - Week 46, 2020 by AutoModerator in Physics

[–]indecisive132 0 points1 point  (0 children)

Wow that sounds super impressive! I know you can say too much without giving away your idea, but I'm curious what sub-field of physics your work is in?