Including bioinformatics into an agriculture/horticulture dissertation project
Entering edit mode
4.4 years ago

Greetings everyone,

After some digging around on the website I've decided to post this question as I haven't found an idea yet and still am pretty clueless how to start. If I've repeated the question then my appologies, feel free to delete it and I'll dig the forum deeper.

I'm in my final M.Sc year doing genetic engineering and have chosen bioinformatics for the graduation project. So far we've learned some basics (like database queries and BLAST) and I've been learning some basic coding for the past year (C# and some R).

The final aim would be to create a bioinformatics project that could be used/involves plant amelioration. I have maximum freedom so any suggestion is welcomed.

Thank you!!!

agrobioinformatics plant-gene-analysis • 729 views
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That's an extremely broad question (more of a forum really). Is the goal to design a project to analyze and perform yourself, or to generate a proposal for something with limitless resources? If you need to perform the actual project then what resources are at your disposal? Are you working in a lab that could perform any informatics experiments? Are you trying to perform a project using only publicly available data? How much time do you have to perform the project?

Aside from the technical/detailed questions above, the more important questions are what you are interested in and want to work on. If you question is just "How can bioinformatics be applied to agriculture" the answer is any way you can imagine. There are thousands of agriculture grants, not to mention all of the proprietary projects going on in industry, and literally millions of potential projects. The important questions to ask are:

1) What aspects of agriculture interest you?

2) What aspects of bioinformatics interest you?

3) What projects intersect those two sets of interest?

4) Which of those projects do you have the resource to pursue?

No forum can answer those questions, it's an opportunity to dig into something you find interesting and have fun with it.

Entering edit mode

I understand and thank you for the detailed answer. Initially I wanted to keep the question short but I see the point now, so here it goes:

Honestly I don't have a specific goal at the moment, but if given the choice and possibility I'd like to design and perform something myself, as the choice is not limited by anything. As my resources are limited (there are no actual bioinformaticians that work in the university) and have nothing to start from then yes, my goal would also be to use publicly available data. The available time would be two months (of fulltime work only on the project and no other distractions).

As the profile of the university/degree is plant genetics/genetic engineering, some of the knowledge gained was in gene expression which I thought was interesting and could be further analyzed using bioinformatics. When it comes to genomes, some horticultural plants (like Maize) have full genomes already sequenced (sometimes even several cultivars) so I thought I could use those for further studying gene expression.

Maybe the answer is still pretty broad, but the project doesn't have to be complex or groundbreaking, that's why any input is highly appreciated.

Thank you!!

Entering edit mode

You're still talking pretty broadly, but it's definitely a start! By gene expression are you interested in transcription regulation, RNA processing, chromatin remodeling/epigenetics, the role of SNPs in gene expression? Are you specifically interested in crop plants like Maize, or are you open to using model systems like Arabidopsis?

I'd recommend taking a week or so and doing some reading through the literature, see what's out there and educate yourself on what types of questions are being asked in the field. Find an interesting paper and circle all the references that pique your interest, then read those papers and circle those references. During this exploration process keep asking yourself what they're doing, why they're doing it, and what you would do differently. If you're just interested in "gene expression" in general, then read papers covering a few different topics and start asking yourself how they might interact. Once you start asking yourself these questions, you can start pulling down their data and trying to answer them.

Maybe you'll read a paper about splicing regulation, a different paper about chromatin modifications and ask yourself if there's a link. If they use the same model and the same controls you can pull down the two datasets and start to compare them. You can use GEO to search for available datasets. Maybe you want to look at H3K27ac after Auxin treatment, just type that in and see how many datasets are available. Read the papers to understand where the data is coming from, but go crazy and have fun with it!

I'd say to definitely invest a good chunk of time being a full time reader, really understanding and outlining what you want to do, but that research phase will pay off later in the project.


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