Bioinformatics / Data Science masters?
I'm finishing up a genetics and microbiology degree at sheffield and have been offered places for bioinformatics at manchester, leicester and cranfield (waiting on QMUL and nottingham). I've also been offered a place for data science at sheffield.
Issue is I don't know what I want to do with my life after so I'm unsure of which course/uni to pick.
In terms of bioinformatics, I'm currently under the assumption that manchester is very well respected for that course in the UK. Data science gives the wider possibility of branching out from molecular biology in the future.
I guess I'm asking for opinions on the courses at each uni or just general thoughts on my situation.
Issue is I don't know what I want to do with my life after so I'm unsure of which course/uni to pick.
In terms of bioinformatics, I'm currently under the assumption that manchester is very well respected for that course in the UK. Data science gives the wider possibility of branching out from molecular biology in the future.
I guess I'm asking for opinions on the courses at each uni or just general thoughts on my situation.
Original post by Sakim
I am in a very similar situation of indecisiveness although at an earlier stage so your experience would be valuable to me, to say the least. What did you end up choosing and why?
Hey Sakim, I'm in a similar position too, I would actually prefer to find a job that allows me to build on bioinformatic skills but they are hard to come by and also masters are so expensive!
Original post by Sakim
I am in a very similar situation of indecisiveness although at an earlier stage so your experience would be valuable to me, to say the least. What did you end up choosing and why?
Sorry, haven't logged in since then. I ended up going with bioinformatics and manchester.
Original post by jackien1
Sorry, haven't logged in since then. I ended up going with bioinformatics and manchester.
Hi Jack, No worries. I am currently doing a master's in Bioinformatics here at Manchester too
Original post by Sakim
Hi Jack, No worries. I am currently doing a master's in Bioinformatics here at Manchester too
how are you finding it?
tip: when it comes to the RPs, don't get kontopantelis as your supervisor.
Original post by jackien1
I'm finishing up a genetics and microbiology degree at sheffield and have been offered places for bioinformatics at manchester, leicester and cranfield (waiting on QMUL and nottingham). I've also been offered a place for data science at sheffield.
Issue is I don't know what I want to do with my life after so I'm unsure of which course/uni to pick.
In terms of bioinformatics, I'm currently under the assumption that manchester is very well respected for that course in the UK. Data science gives the wider possibility of branching out from molecular biology in the future.
I guess I'm asking for opinions on the courses at each uni or just general thoughts on my situation.
Issue is I don't know what I want to do with my life after so I'm unsure of which course/uni to pick.
In terms of bioinformatics, I'm currently under the assumption that manchester is very well respected for that course in the UK. Data science gives the wider possibility of branching out from molecular biology in the future.
I guess I'm asking for opinions on the courses at each uni or just general thoughts on my situation.
I can see from the replies you have made your choice, but just in case anyone sees the thread with similar questions!
Although I haven't done bioinformatics at Cranfield, I have been a teaching assistant on some of the modules for it, and got to know the teaching team for that course.
As with most Cranfield courses, this is quite career-focused, and therefore less restrictive than might be implied by the title 'Applied bioinformatics'.
It has modules on R (commonly used in all sciences for data analysis), python (a favourite for biologists but also many others), java (the developers favourite, and less frequently used in biology, at least in my experience), and machine learning (what an amazing thing to include on any CV!). These skills definitely wouldn't leave you 'restricted' to biology, or any other field
It's also supported by the Cranfield Career Development Service, who can help you tailor your CV to whatever field you are particularly interested in nearing graduation, prepare for interviews, and other help!
Also, there are projects offered to students in collaboration with industry each year, giving an insight into how companies work, and developing links before you leave. Some previous collaborators include Unilever, GlaxoSmithKline, Cambridge University, Sanofi Aventis, and many more.
If you want a more comprehensive list of collaborators, module details, info about the structure and content, the Applied Bioinformatics page is here:
https://www.cranfield.ac.uk/courses/taught/applied-bioinformatics?gclid=CjwKCAiAx8KQBhAGEiwAD3EiPx9g7DRhpLEs3o7bgmwevocsSXy1SvC2Yq201KdzRtM8-a6U7jwbqBoCocYQAvD_BwE
I hope this helps anyone making similar decisions!
Ciara
2nd year Agrifood PhD student
Cranfield Student Ambassador
Original post by S F
Hi there, just looking into bioinformatics masters and I was wondering about the Manchester course, how did you find it? Also random question, are you given a laptop to use for the year from the university?
it was decent, although admin at uom is horrendous and a joke tbh, we haven't gotten/aren't getting physical degree certs (edit and their grad department has yet to reply to multiple emails asking for clarification). if you get a good supervisor and you have interest in your project you're set, but if you get screwed and get allocated a *****y supervisor then you're ****ed (i had a supervisor whom i only had 45mins of meetings (total 2 meetings despite me asking for more) with over 3 months and he would only selectively answer questions in emails, 15/45m of the meetings was an intro call to just say hi).
no you're not given a laptop to use, not sure if they have a scheme for people who can't afford laptops though.
(edited 2 years ago)
Hello, can you please tell me as to how long did you wait until you got an offer after sending an application?
I have an offer from Bristol, Queens University and Liecester. I am yet to get a reply from Manchester or Glasgow (It has not been 20 days yet). Would you prefer Manchester over these?
Original post by meethindocha000
Hello, can you please tell me as to how long did you wait until you got an offer after sending an application?
can't remember, sorry.
Original post by meethindocha000
I have an offer from Bristol, Queens University and Liecester. I am yet to get a reply from Manchester or Glasgow (It has not been 20 days yet). Would you prefer Manchester over these?
manc over leicester, but i'd strongly consider bristol or glasgow alongside or even over manc.
Original post by jackien1
it was decent, although admin at uom is horrendous and a joke tbh, we haven't gotten/aren't getting physical degree certs (edit and their grad department has yet to reply to multiple emails asking for clarification). if you get a good supervisor and you have interest in your project you're set, but if you get screwed and get allocated a *****y supervisor then you're ****ed (i had a supervisor whom i only had 45mins of meetings (total 2 meetings despite me asking for more) with over 3 months and he would only selectively answer questions in emails, 15/45m of the meetings was an intro call to just say hi).
no you're not given a laptop to use, not sure if they have a scheme for people who can't afford laptops though.
no you're not given a laptop to use, not sure if they have a scheme for people who can't afford laptops though.
Thanks for the reply! Just another question, how many hours were you in a week, I'm looking to get a part time job but don't have my timetable yet so it would be great to have a rough idea, thanks!
Original post by S F
Thanks for the reply! Just another question, how many hours were you in a week, I'm looking to get a part time job but don't have my timetable yet so it would be great to have a rough idea, thanks!
you're well into it by now and i actually have no idea if they're doing stuff in person nowadays, but i didn't go in at all till the last 3 months and even then that could've been done remotely. i did my degree during peak covid.
Original post by Amyhouseman123
Hey Sakim, I'm in a similar position too, I would actually prefer to find a job that allows me to build on bioinformatic skills but they are hard to come by and also masters are so expensive!
Hi @Amyhouseman123. Just following up on this message. What have you decided to do in the end? I am currently in a similar position and would really appreciate your advice
Original post by meethindocha000
I have an offer from Bristol, Queens University and Liecester. I am yet to get a reply from Manchester or Glasgow (It has not been 20 days yet). Would you prefer Manchester over these?
In also in a similar situation. I have offers from Glasgow and Bristol and can’t decide on which one to chose
Hi guys, I read the whole thread and it was quite informative, but this also brings me to a similar confusion, I have offers from Liverpool, Bristol, QMUL and Birmingham, although I'm still waiting for a response from Manchester. Which one would you guys suggest (Also I submitted my application to Manchester on the 14th of Feb and it's been more than a month and yet there is no response, I would really appreciate it if someone could clarify this situation regarding the application timeline)
2) Perform homology modelling via web server: SWISS-MODEL.Describe what you have done for this step. Discuss the table of templates SWISS- MODEL returns. Identify any promising templates to be taken further to perform modelling of your target, and explain your selection.
(Hint 1: select at least 1 template here for automated homology modelling.)
3) Examine the model(s) created by the server. Download the PDB file(s) for the template(s) used by the server, as well as the PDB file(s) of the model(s) created by the server.(Save these results, as well as any evaluation plots/statistics SWISS-MODEL returns for your model – you will need them later in this assignment.
4) Perform a BLAST search with the target sequence for structure modelling (using the PDB database of protein structures). Retrieve sequences of suitable templates.Describe the BLAST results.(max. 250 words)
5) From your BLAST search, select the best template(s) for homology modelling.(Hint: select at least 1 template from the BLAST table.)Describe which template(s) you have selected, and justify your selection.
6) Perform T-Coffee alignments of your query sequence and the selected templates.Compare the template(s) hits returned from SWISS-MODEL in step (2), and the one(s) you would have selected based on BLAST and the T-Coffee alignments. Are there any notable differences between T-coffee alignments and SWISS-MODEL alignments and how are these explained?
7) Perform your search for a 3D model via Alphafold2- extract the domain you are interested in.(Save the PDB files of the of the domain/complete protein and explain the Alphafold2 model structure providing the corresponding figures)
8) Examine your models, from both alignment-mode and automated-mode homology modelling using molecular visualisation software (e.g. PyMOL). Perform a comparison (structural, 3D superimposition) with the corresponding templates, and/or any deposited models (e.g. in databases such as Modbase) of your target protein. Analysis in this step can include: i) comparison between the models, ii) comparison between the templates, iii) comparison between the models and the templates. Discuss briefly what each one of these analyses can tell us based on what is relevant for your assigned protein/sequence.a) Display informative snapshots of your structural analysis. Discuss these results, referring, wherever necessary, to other results you have had so far, e.g. the alignments and the BLAST/SWISS-MODEL template hits table.b) Evaluate the model(s) from the parameters provided in the output of SWISS-MODEL.
9) Evaluate the model(s) and template structures with Molprobity.Display results from Molprobity. Discuss these results in light of your structural analyses, as well as your results on the template searches.
10) Search for the functions of your assigned protein.Using public repositories and servers, as well as any literature you have found, comment on possible functions for the gene/protein corresponding to the selected sequence. Provide the interacting partners of your protein in homo sapiens using STRINGDB. If there is no human homolog use the closest human protein identified in blastp.
This is the fasta sequence>XX8QQASATGSISIEEIDLEGKYVQLKNNSEKDQSLGNWRLKRQIGDGEEIAYKFTPKYVLRAQTVTIWGADAGVSHSPPSVLVWKNQGSWGTGGNIRTYLVNSDGEEVAVRTVT
Please can someone provide guidance on how to navigate through these questions. Feeling really stuck
(Hint 1: select at least 1 template here for automated homology modelling.)
3) Examine the model(s) created by the server. Download the PDB file(s) for the template(s) used by the server, as well as the PDB file(s) of the model(s) created by the server.(Save these results, as well as any evaluation plots/statistics SWISS-MODEL returns for your model – you will need them later in this assignment.
4) Perform a BLAST search with the target sequence for structure modelling (using the PDB database of protein structures). Retrieve sequences of suitable templates.Describe the BLAST results.(max. 250 words)
5) From your BLAST search, select the best template(s) for homology modelling.(Hint: select at least 1 template from the BLAST table.)Describe which template(s) you have selected, and justify your selection.
6) Perform T-Coffee alignments of your query sequence and the selected templates.Compare the template(s) hits returned from SWISS-MODEL in step (2), and the one(s) you would have selected based on BLAST and the T-Coffee alignments. Are there any notable differences between T-coffee alignments and SWISS-MODEL alignments and how are these explained?
7) Perform your search for a 3D model via Alphafold2- extract the domain you are interested in.(Save the PDB files of the of the domain/complete protein and explain the Alphafold2 model structure providing the corresponding figures)
8) Examine your models, from both alignment-mode and automated-mode homology modelling using molecular visualisation software (e.g. PyMOL). Perform a comparison (structural, 3D superimposition) with the corresponding templates, and/or any deposited models (e.g. in databases such as Modbase) of your target protein. Analysis in this step can include: i) comparison between the models, ii) comparison between the templates, iii) comparison between the models and the templates. Discuss briefly what each one of these analyses can tell us based on what is relevant for your assigned protein/sequence.a) Display informative snapshots of your structural analysis. Discuss these results, referring, wherever necessary, to other results you have had so far, e.g. the alignments and the BLAST/SWISS-MODEL template hits table.b) Evaluate the model(s) from the parameters provided in the output of SWISS-MODEL.
9) Evaluate the model(s) and template structures with Molprobity.Display results from Molprobity. Discuss these results in light of your structural analyses, as well as your results on the template searches.
10) Search for the functions of your assigned protein.Using public repositories and servers, as well as any literature you have found, comment on possible functions for the gene/protein corresponding to the selected sequence. Provide the interacting partners of your protein in homo sapiens using STRINGDB. If there is no human homolog use the closest human protein identified in blastp.
This is the fasta sequence>XX8QQASATGSISIEEIDLEGKYVQLKNNSEKDQSLGNWRLKRQIGDGEEIAYKFTPKYVLRAQTVTIWGADAGVSHSPPSVLVWKNQGSWGTGGNIRTYLVNSDGEEVAVRTVT
Please can someone provide guidance on how to navigate through these questions. Feeling really stuck
Original post by Sakim
Hi Jack, No worries. I am currently doing a master's in Bioinformatics here at Manchester too
Hi Sakim, I wanted to reach out to get some guidance on a bioinformatics related task, if you are willing/ available to help please. I would highly appreciate
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