This is actually the md readme from the github repo.


Repo for the new site, currently called pedel2 —but will change name when inspired. I assume that it will be hosted as pedel.enzymes.org.nz or similar in the future. See also my mutagenesis repository. It is currently hosted on a Raspberry pi in my flat, hence the subdomain "pi".

To Do list

Sorted by urgency:

  • Theme Get a word from Wayne and Matilda about the theme
  • Pedel-AA a-elements linkage is broken in certain bits. :angry:
  • Pedel range of conditions not done yet, but pedel_batch wrapper made. —original functionality
  • Pedel-AA graphs —original functionality
  • PedelAA links to modals in sub table. — I thought this was done. :confused:
  • QQC wire reverse
  • Glue works, but make it print a graph at different values. —extra functionality
  • driver output could be made into a nice table actually. —extra functionality
  • mutationprimer why is Y66 actually Y67? Does GFP not start from ATG??
  • mutationprimer IDT does not accept lowercase degenrte nts.
  • mutatcaller does not check for terminal indels if set to local. Currently set to global.
  • mutatcaller silent mutations! Also ratio of these!
  • mutatcaller input penalty values for match returns mutations. what the hell does this mean?
  • Scheme 19c and 20c in QQC are incomplete!!
  • js of misc for codon has error due to staticmethod being called... changed the static methods fom QQC.
  • GlueIT in pt needs js to change the number of codons.
  • Glue needs a switch like Pedel —or does Pedel need two pages?
  • URL query string needs to be integrated
  • make size responsive. —why would anyone use their mobile?
  • Make sure code supports badly formatted sequences. e.g. numbers and spaces and newlines.
  • Also edit js side to catch client side errors. —Some do already...
  • Rosetta landscape. Add distribution of mutations and norm thinggy like my matlab script has.
  • Mutanalyst is using old JS still. Not Ajax and python. —Is this actually urgent??
  • mutationprimer. temporary name. Most functions are copypaste jobs of deepscan. —So?
  • mutationprimer code currently written until making a function in mutant_wrapper... —what does this mean?

Bullcrap area


  • How can I use Seen.js for a landscape? And when is a 3d rotatable terrain better than a 2D plot? Aka. is it a load of pointless glitz?

Next Gen mutantcaller

Pipedream. fastq files are several GB big, thus they cannot be uploaded. However, a small simple custom alignment algorithm running with GPU.JS could do it quite fast.

Benchling integration

NB. Benchling API: Benchling API reqires a key. This seems to be issued on request to devs. SO this is not an option.