Developing algorithms

Question

[jenny_govind]

Hello everyone, what factors must be considered when developing an algorithm for microbial genomics?

[Ram]

For one, the problem statement needs to be much clearer. An algorithm is a step by step approach to solve a specific problem, and your statement here is looking for a step by step approach to an entire field, which will give you a meandering roadway that gets you everywhere and nowhere all at once.

[jenny_govind]

This is the title that was given to me for a presentation for an internship. I think they deliberately kept it vague.

All they told me that it should be related to outbreak situations or antibiotic resistance.

[GenoMax]

So you have a specific goal, which is great. Ram has outlined what is needed to create an algorithm.

An algorithm is a step by step approach to solve a specific problem

Now you need to do some background research on antibiotic resistance e.g. what causes it, how to find the causes for it, what kind of experimental/informatic data you will need. Then put a plan together to work towards that goal.

[jenny_govind]

It's starting to make a lot more sense now, thank you so much!

[Joe]

Agree with Ram, I think this is much too vague to be useful, however if you pick a toy example, there are some unique hallmarks of microbes that they might be probing for here.

For example, doing phylogenetics is an almost uniquely difficult problem in microbial genomics, because there is so much horizontal gene transfer (as opposed to vertical). Thus, any algorithm you were to develop which addressed this sort of challenge would need to factor in this trait of microbes.