GC Content % and averages

I’ve got my plotly chart displaying when there are GC Content window percentages that are above or below a user specified threshold. This might need tweaking, and I’ll try and get some feedback during the mock mid-project demonstration I have on Friday from Amanda and the other people what could be done. I will also clean up the web page design and layout before then, this is just a basic start.

Things I want to get done before Friday:

• Create artificial contigs for use and testing
• Write more tests for the GC content checking
• ORF results
• Display ORF results with the GC content chart
• Create some slides for explaining metagenomes, the project and its aims
• Allow user to upload a FASTA file or paste their contig directly
• Make the page look prettier

With those done I’ll feel a bit more comfortable about giving my mid-project demo.
After that it’s working on the Job Application assignment for Prof. Issues due next week, work on anything that comes from feedback from the mock mid-project demo and then clean up the slides and notes for the actual mid-project demo on Monday.

At some point after that, I plan on going through everything I’d done so far and turning my Stories and tasks (currently loose paper) into something electronic I can keep track of. My process has slipped a bit, but I’ve started using pomodoro technique to get back on track with dealing with working through things at a steady pace.

Thymeleaf and Plotly

I’ve been messing with getting my stuff working in Java Spring Boot, for the main reason that I wanted to display my results from Java in a nice way (and what better way than a browser using Javascript).
While I’m aware there are other options (no web at all, instead make a GUI using a Java library, using Ruby/Rails), I figured it would be a good opportunity to learn a new technology (Spring Boot) while using something I enjoy programming in (Java, Javascript, HTML).

I wrestled with getting my results to display for a while, and configuration was shown as many, many different ways when looking at examples of how to set up Thymeleaf. I also think due to my lack of experience with Thymeleaf, there were a lot of moments when I was probably close to my desired result, but messed up my code somewhere so missed the mark.

Anyway, it works, horay! I’ll show examples later as I’m being kicked out of the room I’m typing this in. 😀

Project Poster & Spring Boot

Very small update:

Been working on my Project Poster and got some feedback from Amanda. It’s due tomorrow and I’ve got a couple of changes to make. Should be okay. Not totally happy with it, but aside Amanda’s changes I’m at a bit of a loss with it.

I’ve started working using Java Spring Boot. I wanted to look for a decent way to display the report, and then I found nice web things (Plotly.js), but didn’t want to move my code over from Java to Javascript. So, using JSB I should be able to tie them together instead. In theory anyway. I’m pretty clueless about Spring Boot, but I’m going to give it a go anyway and see how I get on.

Once that’s done and the poster is submitted I can get back to working on ORF highlighting and generating artificial metagenomes.