Metadata-Version: 2.4
Name: emusynth
Version: 0.1.0
Summary: Host-side streamer for the emusynth ABI 3400 solenoid emulator
Project-URL: Repository, https://github.com/saarantras/emusynth
Author-email: Mackenzie Noon <mackenzie.noon@yale.edu>
License: MIT
Keywords: abi-3400,arduino,dna,serial,synthesizer
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: System :: Hardware
Requires-Python: >=3.8
Requires-Dist: pyserial>=3.5
Description-Content-Type: text/markdown

# emusynth -- Notes / parking lot

Things we've decided to defer but should come back to soon.

## Next target devices to model (after the 3400 baseline works)

The 3400 is a fine prototype for control-system architecture but caps at
~200 nt phosphoramidite chemistry. To exercise the design at higher fidelity
toward "modern long-read synthesizer" use cases, the next manuals/specs to
chase:

### Tier 1: realistic, public docs, similar architecture (still phosphoramidite)
- **BioAutomation MerMade 192 / 384.** High-throughput phosphoramidite, 192
  or 384 parallel wells, large valve array. Manuals circulate on used-equipment
  sites and in core-facility documentation. Same chemistry as the 3400 (still
  ~200 nt cap) but the valve multiplexing is much wider -- forces the decoder
  to handle a real well-select space, not just 4 columns. Best architectural
  step up.
- **PerSeptive / ABI Expedite 8909.** Sibling of the 3400, abundant docs, well
  understood. Useful as a sanity-check / portability target for the existing
  procedure tables.
- **GE/Cytiva AKTA Oligopilot.** Gram-scale phosphoramidite, packed-bed
  reactor (different topology). Manuals public. Useful if we want to model
  manufacturing-scale rather than research-scale.

### Tier 2: real long-read targets, harder to access
- **DNA Script SYNTAX.** Benchtop enzymatic (TdT), commercial since ~2021,
  currently ~80 nt and extending. User manual gated behind customer support.
  Workaround: DNA Script's **patent portfolio** describes their fluidics
  in block-diagram detail. Search Google Patents for assignee="DNA Script"
  with terms like "fluidic", "reactor", "synthesis cycle". Patents are nearly
  as good as a manual for our prototyping needs.
- **Ansa Biotechnologies.** Service-only (no benchtop). Same patent strategy.
- **Molecular Assemblies.** Service-only. Same patent strategy.

### Tier 3: academic / open
- Palluk et al. 2018 (Nature Biotechnology) -- foundational TdT enzymatic
  synthesis paper. Describes chemistry + reactor in enough detail to write
  a "v3 enzymatic" procedure table.
- DIY synbio community projects (Hackaday, GitHub). Variable quality, none
  are kilobase-class.

## Recommended sequence of next iterations

1. Finish 3400 model (where we are now): LEDs, Pi decoder, end-to-end test.
2. **MerMade 192 model**: same chemistry, much wider valve multiplexing.
   Stress-tests the decoder's ability to handle many parallel wells.
3. **Enzymatic v3 procedure table**: built from DNA Script + Ansa patents
   plus the Palluk paper. Demonstrates chemistry-agnostic generality of the
   architecture (same Uno, same Pi decoder, just different `Step` table).
4. Decision point: continue refining the emulator, or start designing real
   hardware for one of the above chemistries.

## Other deferred items
- Multi-column parallel synthesis on the 3400 (interleaved column-select).
  Currently v1 runs one column per RUN/STREAM.
- Modified bases (positions 5-8, valves V27-30) for labeled / non-canonical
  nucleotides.
- RNA and phosphorothioate cycle scripts (LV200-RNA, LV200-PS).
- Standalone operation (no host computer) -- requires moving from Uno to a
  board with more SRAM (Mega 2560, Teensy 4.x, ESP32) so the full sequence
  can live on-instrument again. Streaming protocol stays as the primary path.
- v2 hardware: 24V realistic solenoid drive + PC817 opto level-shift to Pi.
  Sketched in WIRING.md, not yet built.
