Moritz E. Beber

You should see the solver output in the terminal where you started the Jupyter notebook.

Usually, not having bokeh is a warning. So either you are importing a part of cameo that requires bokeh or something in your environment is turning warnings into errors. You...

Hi, you can 'apply' a pathway to your base model and then optimize for the pathway target. That will give you the theoretical maximum flux through your heterologous pathway. Higher...

Randomly saw the call on Twitter. I'm not familiar with Bluesky but I'm working on a similar project myself so I'm happy to review this. My project is for internal...

Randomly stumbled upon this issue and just wanted to note that `return NotImplemented` has a different purpose. It is not to mark abstract methods but to mark a certain comparison...

Happy to answer your questions: * I ran every process sequentially in order to not affect bandwidth. * In the plot in the readme are the times (durations) recorded of...

I see, I had understood parallel-fastq-dump as a "complete package" so I hadn't considered using prefetch first.

> another interesting point is using `--gzip` or `--bzip2` on parallel-fastq-dump, for big SRAs the size difference between compressed and uncompressed fastq can be very big, so writing compressed files...

Alright, I've made a new benchmark first using `prefetch` for all tools and also including compression. I have summarized the results in the readme https://github.com/UnseenBio/sra-demo-benchmark/tree/benchmark-prefetch

I think you make very valid points. I'm currently limited to one desktop computer, though 🙂 So the combinatorial increase in jobs and threads is a bit much for that....