jvrana/DASi-DNA-Design

Issues

• better parallelization

  #55 opened 4 years ago by jvrana
  1

• dasi.exceptions.DasiSequenceDesignException: Sequence is cyclic but there are no precessors for AssemblyNode(index=0, expandable=True, type='A', overhang=False)

  #54 opened 5 years ago by jvrana
  0

• Long Gibson Assembly Parameters should be different than short gibson assemblies

  #52 opened 5 years ago by jvrana
  0

• Designs should keep record of errors (instead of raising Exception)

  #51 opened 5 years ago by jvrana
  0

• Annotations on SeqRecords are not being carried through to output.

  #50 opened 5 years ago by jvrana
  0

• Users should be able to control thresholds for valid primer pairs

  #49 opened 5 years ago by jvrana
  0

• Add examples module users can pull from to test out DASi

  #48 opened 5 years ago by jvrana
  0

• Information about input sequences should be present in

  #47 opened 5 years ago by jvrana
  0

• Bug: `Sequence is cyclic but there are no precessors` error

  #46 opened 5 years ago by jvrana
  0

• Attach notes to edges when efficiency is adjusted in Graph post processing

  #45 opened 5 years ago by jvrana
  0

• Find invalid assemblies

  #44 opened 5 years ago by jvrana
  0

• JSON Schema display in Sphinx should be more condensed

  #43 opened 5 years ago by jvrana
  0

• Improve Documentation

  #32 opened 5 years ago by jvrana
  0

• DASi should issue a warning for highly complex repetitive sequences before transformation into bacteria

  #41 opened 5 years ago by jvrana
  0

• Invalid fragment PCR products are produced.

  #26 opened 5 years ago by jvrana
  0

• SBOL Output

  #33 opened 5 years ago by jvrana
  0

• Better Integration between Aquarium <> Terrarium <> DASi <> {Benchling, SynBioHub}

  #40 opened 5 years ago by jvrana
  0

• Clean up integration IO for DASi

  #39 opened 5 years ago by jvrana
  0

• Understand why some designs fail to assemble

  #38 opened 5 years ago by jvrana
  0

• Preferrably tests short tests in automated CI

  #37 opened 5 years ago by jvrana
  0

• DNA complexity tests sometimes fail

  #36 opened 5 years ago by jvrana
  0

• Randomized tests occassionally fail

  #34 opened 5 years ago by jvrana
  0

• Randomized tests occasionally fails

  #35 opened 5 years ago by jvrana
  0

• Testing Utilities: More control over random library generation

  #27 opened 5 years ago by jvrana
  0

• Shared sequence cost often does not match final cost

  #30 opened 5 years ago by jvrana
  0

• Better explaination for DASi design failures

  #29 opened 5 years ago by jvrana
  0

• JSON output schema

  #28 opened 5 years ago by jvrana
  0

• Input parameters should be exposed

  #25 opened 5 years ago by jvrana
  0

• Vendor Configurations (e.g. IDT, Twist)

  #23 opened 5 years ago by jvrana
  0

• speed improvements

  #22 opened 5 years ago by jvrana
  0

• Implement DNA complexity to efficiency for graphs

  #14 opened 5 years ago by jvrana
  0

• Better Logger

  #21 opened 5 years ago by jvrana
  0

• PDF Assembly Reports

  #18 opened 5 years ago by jvrana
  0

• Implement sharing of primer and PCR product design

  #17 opened 5 years ago by jvrana
  0

• Implement DNA Synthesis Sharing

  #16 opened 5 years ago by jvrana
  0

• RuntimeWarning: invalid value encountered in true_divide

  #15 opened 5 years ago by jvrana
  0

• Optimal Partitioning Schema

  #13 opened 5 years ago by jvrana
  0

• Gap Synthesis Complexity Span Cost

  #7 opened 5 years ago by jvrana
  0

• Linear DNA Design

  #10 opened 5 years ago by jvrana
  0

• Degenerate designs

  #9 opened 5 years ago by jvrana
  0

• Implement tblastn for CDS searches

  #8 opened 5 years ago by jvrana
  0