Timothy R. Fallon, PhD

Including in Biopython?

1

Hi there, Thank you for making pydna. I've had fun using it to automate some cloning reactions. It seems like pydna is something that really should exist in Biopython proper....

Augustus PPX mode: augustInvalid block no. error

2

Hi there, I've made a small prototype Nextflow pipeline to run Augustus in PPX mode with custom protein profiles, via Docker or Singularity: https://github.com/photocyte/luciferase-PPX-predictor-nf ( Augustus Docker image from `quay.io/biocontainers/augustus:3.4.0--pl5321hd8b735c_3`...

### PLATFORM (Mac, PC, Linux, other): Mac ### OPERATING SYSTEM (eg OSX 10.7, Windows 8.1): 10.15.1 (Catalina) ### SEVERITY (Critical? Major? Minor? Enhancement?): Minor ### DESCRIPTION: Hi there, thanks for...

HTTP/3 or QUIC support?

3

Hi there, Thanks for working on Jupyter Server! I really enjoy using Jupyter (Lab) in my work. One issue I have sometimes encountered, is my unoptimized/verbose scripts pump too much...

Lag on machines with non-integrated GPU

15

Hi there, thanks for working on Antares! A true blast from the past... The 0.7.3 release works great, recently played through the whole original scenario on a Retina MBP running...

Hi there, A breaking change in `argh` seems to have impacted `gffutils-cli` : https://argh.readthedocs.io/en/latest/changes.html#version-0-30-0-2023-10-21 ``` mamba create -y -p gffutils_cli_env2 'argh>=0.30.0' 'gffutils' conda run -p ./gffutils_cli_env2 gffutils-cli children symlinks/{gff_name}.db {transcript_id}...

Oval or diamond/octagon in addition to arrows for displayed features?

1

Hi there, I've been using DNAFeaturesViewer for visualizing domains on polypeptides. (Yes, not exactly it's the intended use case of DFV - but its seeing as FASTA & GFF files...

genometools was taking a long time to install (and I already had it via conda anyway), so I figured I'd slightly modify the install script so it could install only...

Issue a release & publish on Bioconda?

1

Hi there, Big fan of flo. Has worked really well for my research. But it would be even better if flo were on bioconda and had its dependencies explicitly linked,...

SO sponsorship for submission of bioinformatics file formats for IANA Media Types ("MIME") registry?

2

Continuation of this email thread with keilbeck&genetics.utah.edu & evan.christensen&utah.edu, from tfallon&ucsd.edu. That thread resolved to give a shot at SO sponsored submission of bioinformatics file formats to the IANA Media...