Ask Me Anything About Bioinformatics #3

[@DataProfessor]

👉Watch this video next (How to learn data science in 2021) kzbin.info/www/bejne/pYOZaGOKrdybbpo Support this Channel 👇👇👇 🌟 Buy me a coffee www.buymeacoffee.com/dataprofessor 🌟 Download Kite for FREE www.kite.com/get-kite/? 👉 Subscribe to this KZbin channel kzbin.info 👉 Join the Newsletter of Data Professor newsletter.dataprofessor.org

[@username42]

0:18 Look mom, I'm famous🤩 also thank you for the detailed explanation in the video :)

[@DataProfessor]

Haha, Yes you are! Thanks for the question 😊

[@gersonmatavele80]

Thank you for this useful channel , professor.

[@DataProfessor]

You are very welcome 😊

[@fabsync]

Love your videos! I would love to see new videos on how (so many ideas) to go about "improving" materials like "graphite" for example for better batteries

[@DataProfessor]

Hi, thanks for the suggestion. That may be outside my domain, sounds like material science. I would think that an important molecular property to look into would be the molecular orbital energies (e.g. HOMO and LUMO, the highest unoccupied molecular orbital and the lowest unoccupied molecular orbital), which corresponds to the electron-rich and electron-poor states/portion of a molecule.

[@fabsync]

@@DataProfessor man I have been searching for another professor here in youtube with similar approach to teaching material science and nothing!! Do you know of anyone that you can recommend in any platform?

[@neeharika12]

Hi, Prof. Are you planning to do a project on Gene sequencing? or if possible may you connect me to a link where I can learn machine learning with gene seq data? I really liked your drug discovery project. Thanks

[@nb6808]

Hey Data Professor, I am thinking about pursuing a msc in bioinformatics after my bsc in biology. My desired master focuses a lot of on the system biology/medicine side of bioinformatics. Is it a good field to go into? also, is there also an application of bioinformatics in fields like neuroscience, since they also deal with large networks?

[@DataProfessor]

Hi, yes neuroscience is a big field especially for bioinformatics as well as informatics in general. There are also several dedicated scientific journals for the neuroscience domain e.g. www.frontiersin.org/journals/neuroinformatics www.springer.com/journal/12021 www.frontiersin.org/journals/neuroscience www.journals.elsevier.com/neuroscience www.nature.com/neuro/

[@sebastiancastro4126]

I would like to know how do you calculate 3D Descriptors using RDKit. Thanks!

[@DataProfessor]

Hi, 3D descriptors typically require some form of geometry optimization in order to obtain a low-energy conformer (a molecular structure having low and optimal energy), such structure are then used for calculating the 3D descriptors. Thus, at a high-level, the SMILES would have to be converted to a 3D structure then subjected to geometry optimization and finally the low-energy conformer are finally used for calculating the descriptors.

[@adele7718]

Hi Data Professor, Do you have any advice for someone with a molecular biology background considering a Bioinformatics PhD? What do you think are the most relevant research/development areas that will meet industry needs in the near furture? Thanks!

[@DataProfessor]

Some of the hot areas in Bioinformatics is precision medicine, metagenomics and computational drug discovery. At the core of all these is systems biology (network analysis) which would help you to understand the essence of biochemical pathways which can be widely applied for development of therapeutic drugs, etc.

[@adele7718]

@@DataProfessor Thank you!

[@777guy1]

Hey there professor, I have a couple of questions regarding the field of Bioinformatics. So before I ask the questions, I wanted to explain a bit of my situation. I graduated from Uni with a bachelor's of science in bioinformatics back in 2019, and have since then have not done much in regards to bioinformatics and it is mostly due to me not knowing how or where to start. I have looked for jobs in bioinformatics close to me but out of the little I find, most of the time I never hear back from the companies. I notice that most binf jobs require a master's degree which has led to to consider taking a master's course at some university. However I am conflicted with going back to school because I feel as if it is not required given that there are a lot of binf projects one can do at home. I basically feel stuck in that I can't get a proper response from an employer and I suspect it is due to my lack of experience of which I don't know how to acquire. Given this I have started considering applying for other jobs that are not related to the binf field as a way to start getting money which is a bit depressing. So my questions are this: Should I go back to school to pursue a graduate degree ? How can I gain experience in bioinformatics of which I can add to a resume to make me more appealing to employers? Lastly, I feel as if I might not be looking for jobs correctly. I mostly go on Indeed or google and search for bioinformatics jobs. so my last question is: How do I search for bioinformatics jobs? this includes private and research jobs. Thanks for reading this comment.

[@akhilesh_39]

Hi Professor, May I know in bioinformatics what's the size of the data you guys deal with usually?

[@DataProfessor]

This varies with project. Most don't exceed 100,000 compounds and each compound can be described by 100-1000 descriptors. Sometimes we perform cross-products and the number of descriptors can go to the 10,000-100,000 descriptors.

[@akhilesh_39]

@@DataProfessor Thank you.

[@adele7718]

Another question please. For someone going into bioinformatics industry, is it more profitable to learn data science/ML or software engineering skills? Thanks again!

[@DataProfessor]

Here's my take on this, If monetary profit is concern, data science and software engineering may very well lead to higher salary. As for bioinformatics, the salary would be moderately good while the resulting bioinformatics work would ultimately contribute to the development of new drugs and cure of disease (a societal profit).

[@catherinemangare1445]

Hello data professor, I need python or R codes for learning Graph Neural Network or Network analysis Drug Repurposing for SARS-CoV 2

[@DataProfessor]

Hi, I've made a video about an excellent resource that provides codes to various ML implementation mentioned in research papers, please check it out here kzbin.info/www/bejne/ioaWnKKGrquNnNk

[@rawanissa3909]

Hello ! I’m an undergrad bioinformatics student and I have this assignment where struggling to compute petitjean index using python can you help me or give some advice

[@Sukoon_Shubh]

Hello sir this is Priyanka already completed my graduation and postgraduation in bioinformatics but still struggling because there is not much scope in our country and infact some labs like CSIR and many more they are considered much belongs from Life sciences not specifically in bioinformatics so could you tell me about some institutions or lab in india where I can apply.

[@nishirajnikku969]

I am planning to learn Bioinformatics...pls help..Thanks in advance.

[@DataProfessor]

Hi, this is the place to learn bioinformatics. Ask your question, and I will answer 😊 I also made a video playlist teaching about Bioinformatics here bit.ly/dataprofessor-bioinformatics

[@nishirajnikku969]

@@DataProfessor .. sure... I will start going through the play list mentioned above and i will keep posting my doubt......Thanks in advance.

[@angsumandas1]

#Ask_me_anything :- Please tell us what are the other use of data science in biology except drug-discovery and genomics? I often observed these use but I am keenly interested in knowing further!

[@ergosumdre]

Can I run my R code on a GPU?

[@DataProfessor]

Though I haven't tried this out yet, you might want to check out this webpage for further details on GPU in R dept.stat.lsa.umich.edu/~bobyuen/gpuwiki/

[@mandarvaidya7947]

first 😂🤟

[@DataProfessor]

Yay, thanks for the first comment! 😊