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Thank you! 🙂 and let me know if you have any questions

Thanks for pointing that out! Ok I have fixed those links.

​@@MikeSaintAntoine Its still not working. Khan Academy, all links are not working. Please check it again.

@@traveller_of_lyf I think your browser is probably displaying the non-updated version because it's saved in the cache. Can you try either hard-refreshing or clearing the browser cache? Either that or maybe it's just taking awhile to update, so maybe try again in a couple hours.

​@@MikeSaintAntoineGot the updated list now! Thank you so much.!!

@@traveller_of_lyf No problem!

Hi! To find the equilibrium point, you need to set all the ODEs equal to 0 and solve. You could attempt to do this with a pencil and paper, but if it's a complicated system that might not be feasible so you could also do it with a numerical solver in Python. For example, I think the fsolve() function in scipy.optimize could be used for this: docs.scipy.org/doc/scipy/reference/generated/scipy.optimize.fsolve.html If you need any help with the code, please feel free to email me at mikest@udel.edu and I can try to help. And yeah a lot of people have requested a video on how to make a bifurcation diagram so I'm going to try to make that once I have some time. Thanks for watching! 🙂

@MikeSaintAntoine Hi! Thank you very much for your response and guidance. You are very gentle. I will try to do it based on the example you gave, but I will contact you when I need help. Thanks. 🌸 Well, after finding the equilibrium point of the 1st differential equation, should I substitute it in the 2nd differential equation and so on, substituting the 2nd in the 3rd and finally the 3rd in the 4th?

@@cigdemyalcn7665 No problem! The thing is, you need to find the parameters that make ALL of the differential equations equal 0. So if it's an easy system (like the predator prey model) then doing them one at a time like that could possibly work. But if it's more complicated, then the numerican methods like scipy.optimize.fsolve() will just do them all at the same time automatically. Anyway yeah feel free to send me an email if you run into any problems and need help. And happy new year!

@@MikeSaintAntoine Happy New Year to you! I understand, thank you very much again. See you. ☺️

Hi! Can you please email me your code and I'll take a look to see if I can figure it out? My email is mikest@udel.edu

Hey, thanks for watching! Yeah I can definitely try to give some advice. It really depends on what you're trying to do. If you're looking for a job in industry, like a pharma or biotech company, then it sounds like you're already in a good position to start applying for jobs and start working once you finish the master's degree. However if you're looking for a career in academic research, like becoming a professor/PI at a university, then the next step would be to apply to PhD programs, and it sounds like with your background you're in a good position to do that too. So I think it's a matter of just deciding which career path to go down. Or really my advice would be to apply to BOTH jobs and PhD programs, to see what opportunities you get and keep all your options open. Anyway good luck! If you have any specific questions or specific topics you want advice on, feel free to email me at mikest@udel.edu and we can talk further. 🙂

The m3’s graphics card is integrated into the cpu. It’s not an actual gpu. Only an integrated gpu which is not comparable to an actual gpu. Amd is a very close competitor with NVIDIA. I think that amd is going to push past NVIDIA soon, because NVIDIA is adopting the intel model of just shoving as much power as you can through it. That being said NVIDIA have a new line of gpus rumored for 2026 so maybe they’ll shock us.

Because this isn't an Apple bubble marketing ad, but an eyeopener what the right tool for the job can do.

Thanks for watching! 🙂

You can use any windows laptop with mobile gpu and it will be a massacre

Yea it’s not even an actual gpu. It’s an Integrated gpu.

Thanks for watching! 🙂

No problem, thanks for watching and let me know if you have any questions 🙂

No problem, and let me know if you have any questions! 🙂

Thanks and let me know if you have any questions! 🙂

No problem and let me know if you have any questions! 🙂

Ok, I'll try to make some more in the future!

Hi Harsha, sorry about the late reply! Unfortunately I don't really have a good answer to this question. Usually you have to kinda look around the other files they have posted, and try to find the one that has the relationship between sample labels and treatments. Or if you can't find it, try reading through the methods section of the paper to see if it's there. I purposely picked a nice and easy dataset to work with for this video series, but unfortunately sometimes it's not so easy to find all the information you need for the analysis. Good luck with your research!

Thanks for watching 🙂

Hi, sorry about the confusion! I put on the plot axis label that the unit here is in the hundreds, so the predator population was starting at 1 (hundred) and the prey population was starting at 10 (hundred). But I forgot to actually say this! So good point, yes if it was just one predator then it wouldn't make sense because they would't be able to reproduce.

@@MikeSaintAntoine if x=initial number of predators and y=initial number of prey do we always start by getting to a situation where x=1? it seems that this makes the calculations easier because x*y=y, am I thinking correctly?

@@ciferusbux Note that the values of x and y in this model are not necessarily integers. For example, x could be 327.61325.... The model isn't meant to provide an exact number of predator/prey at a certain time, it is meant to demonstrate the overall trends in the population change over time. Hopefully that helps.

Hi, off the top of my head I'm not sure what the error could be. If you've copied the exact same code I used and are still getting an error, that could be because we're using different versions of the same package, like maybe you have an older version, or maybe you have a newer version and they changed something so that my original code no longer works. Could you send me your code to take a look at? My email is mikest@udel.edu. Then maybe I'll be able to reproduce the error and fix it. Thanks!

Hi, yeah that's a good idea, I'll try to make a video on GSEA in the future!

Hey Zubair, good question and definitely not silly to ask! Yeah that part is a bit difficult to understand and it took me awhile to wrap my brain around it myself. I think a good first step is to understand exactly what we're trying to do when we randomly pick the next event. So basically we want to randomly pick the next event with a random draw, but with probabilities weighted according to the rates (also called "propensities"). And these rates change because they depend on the current level of X, so we need to calculate them again each time. So let's say that we're choosing the next event, and and we calculate that the rate for production is 2 (actually it will always be 2 in this example because it doesn't depend on X), and the rate for degradation is 1 (0.1 * X where X=10, for example). So knowing that the rate of production is 2 and the rate of degradation is 1, we want to randomly pick which event will happen next. So basically we convert these into probabilities by dividing the rate of each reaction by the sum of all the rates. So the probability that the next event will be production is 2 / (2+1) = 0.67. And the probability that the next event will be degradation is 1 / (2+1) = 0.33. So basically we want to choose the next event with a random choice, weighted according to these probabilities. The for-loops are just a way of doing that -- randomly picking a next event, weighted according to the appropriate probabilities. It's a little tricky to understand, but if you work your way through it, maybe on paper with the simple example, then you'll see that the first if-statement turns out to be true 67% of the time for the example I just gave, and the elif-statement turns out to be true 33% of the time. Note also that in this simulation with only 2 events we don't even really need the elif-statement. We could have just said "else" and left it at that. But I put the elif statement to show the general pattern, because it we had more than 2 events we'd need to put an elif-statements that follow that general pattern. Anyway, very good question. Yeah wrapping your head around the if-statement checks here can be a little tricky, but I think they key takeaway is that they're just picking the next event randomly, with probabilities that come from the relative rates of the reactions at this point in the simulation.

@@MikeSaintAntoine Ahhh I see. I think now I'm getting the gist of it. After playing around with different values for rand product on paper just like you said, I started to see how the value is weighted within the scope of probabilities of each reaction event. It's a bit tricky indeed but now I'm actually getting hang of it. Thank you so much for taking the time to break it down for me. As someone from medical biotech field it's not so very often for me to deal with such mathematical concepts. But you're making it digestible for us 😄. Please keep doing the good work!

@@zubairhasan9434 No problem, and let me know if you have any more questions! 🙂

Hi! Sorry but I don't think I really understand your question. Could you give me some more details on what you're trying to model? But generally a good way to see if this model applies to a dataset is to just plot the data and check it visually -- does it look like the population is increasing exponentially at first, but then leveling off at a carrying capacity?

Yeah there's a actually a hypothesis in economics that stock prices tend to follow a random walk: en.wikipedia.org/wiki/Random_walk_hypothesis so good observation! Thanks for watching 🙂

I'm not really in a good position to make an IDE video because I actually just use VSCode for writing Python, and don't really use any of the fancy extra features. I just use it like a text editor really. I know there are some pretty advanced IDEs for Python with built-in debuggers and stuff, but I don't really use them. But yeah in the future I can try to make some videos on dataframes / Pandas library. Thanks for watching! 🙂

Hey Arpit, yeah sure just email your code to me at mikest@udel.edu and I'll take a look!

Hi! Unfortunately I don't have a Windows or Linux computer so I won't be able to actually make a video on that. But my guess is that it's probably the same -- you should be able to install Python from python.org, and when you download and install it should give you the IDLE application automatically.

Yes, I'll try to make something like that in the future! I've actually already made a series like that in R, but I'd like to make one for Python too.

Hi, very sorry about the late response! Are you talking about "sample" in this block of code? for(sample in samples){ tmp <- unlist(strsplit(sample,"_")) classes <- append(classes, tmp[1]) } If so, "sample" is just the temporary variable we're using to iterate through the items in the "samples" vector. So basically it's getting assigned to each item in "samples" with each pass of the for loop. Does that make sense? I hope I understood your question correctly, but please let me know if you're still confused and I can try to explain further. Thanks for watching! 🙂

Yeah, good point!

Thanks for watching! 🙂