[HN Gopher] Show HN: PlasCAD: Open-source plasmid editor
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Show HN: PlasCAD: Open-source plasmid editor
Hey! This is an open source plasmid and vector (Short, often
circular segments of DNA) editor, with features related to primer
quality checks, PCR cloning, and protein analysis. I plan to add
more restriction-enzyme-based features in the near future. It has
some extras like a solution-mixing helper, automatic feature
annotation. From a technical standpoint, this is a standalone
binary written using the EGUI library in rust. A project goal is
performance, with small memory footprint, and small application and
file sizes. This is a continuous work-in-progress, and I'm open to
any and all feedback, criticism, and requested features.
Author : the__alchemist
Score : 82 points
Date : 2024-09-03 14:38 UTC (8 hours ago)
(HTM) web link (github.com)
(TXT) w3m dump (github.com)
| samuell wrote:
| Looks cool, and definitely like the standalone binary format.
|
| Tangentially, glad to see more biotech stuff finally making the
| front on HN! :D
| a1o wrote:
| This install part REALLY needs to improve. Give me screenshots of
| how to use this on Windows. Explain step by step. Does
| installation requires administrative credentials or I can run
| this as a lowly tech on the locked down computer the laboratory
| has?
|
| Overall the readme should cater for biologists, biochem and
| others that don't necessarily are well versed into computer
| science. Just explain the basics to get things going.
|
| Also a video would help too - in addition, not as sole resource.
|
| Looks interesting but too out of reach for a regular biochem grad
| to pickup as is.
| the__alchemist wrote:
| Hey! This is a standalone executable; you download the zip
| file, unzip it, and double-click to run. I was thinking about
| instead making it into a minimal installer that would move the
| program to C:\Program Files\PlasCAD or similar, then set up
| shortcuts and file associations. (There is something similar
| for Linux).
|
| Did you hit a snag in that process? This sort of feedback is
| helpful, as you may have hit issues I haven't when testing.
| colechristensen wrote:
| I think it's just someone being overly critical in a way
| that's more than a bit silly.
| lionkor wrote:
| 1. download 2. extract 3. double click to run
| ThrowawayTestr wrote:
| Can't wait until I can 3D print my own proteins.
| isoprophlex wrote:
| One prion disease, please!
| the__alchemist wrote:
| It would be cool to have a compact, cost-effective automated
| recombinant DNA + protein expression/purification workflow! To
| do this currently involves a series of steps, reagents,
| equipment etc.
| colechristensen wrote:
| This is basically what this is. It is very cheap to get
| plasmids manufactured which you can then put into e coli or
| whatever which will build your proteins for you.
| Bjartr wrote:
| You can! You're doing it right now!
| samstave wrote:
| Sorry is this is a lame Q:
|
| Could you take the sequences and python up a blender script that
| will model the thing?
|
| Also, on solutions-mixer- can I use this to map proteins to feed
| to stem cells to get them to present in a certain way?
| the__alchemist wrote:
| Not a lame question at all. For modeling, are you referring to
| protein products, or something different? If so, the answer is
| yes for known proteins; it includes a workflow to download
| structure coordinates from PDB based on an amino-acid sequence
| query. You can currently click a button to download these
| coordinates, and another to open a browser with the PDB
| sequence viewer open to it.
|
| It would be possible, as you said, to add functionality to open
| a script using Python/Blender or similar to view these, or even
| integrate 3D graphics directly in the program. Drawing color-
| coded molecules would be straightforward, but cartoon drawings
| etc would take more work. Modelling unknown/custom proteins
| would presumably require something like AlphaFold integration.
|
| The solutions mixer currently is just for molarity
| calculations. Like, you are making a buffer that contains 300mM
| of this, 100mM of that. It will tell you how many grams or mL
| to add of each reagent. That's a great idea re more practical
| workflows like presenting in stem cells! Should add more to
| that effect.
| samstave wrote:
| There was a research from UCSF that I met when we were
| building that DOgPatch facility in Sf...
|
| She had written a program in python to pipette tiny amounts
| of proteins via tubular matrices valve thingy she made which
| allowed her to feed various proteins to stemcells via her
| little 3D printed tubes and then was researtching what each
| proteins made the stemcells behave like, what they presentd,
| her quote was "what do we need to ffed the stemcell to become
| a heart muscle."
|
| Ive alwasy been intriugued by this as I want to experiment
| with my own stemcells.... specifically in ocular regen.
|
| But having AI craft blender snippets has been super simple to
| get it to draw geometry - so a GPT that can translate between
| some chemistry constraints to 3D- molocule constraints - plus
| there are a bunch of 3D chem libraries (there was an
| interesting one on HN a while back that I commented on a
| bit..)
|
| What would be interesting would be a version of 'meta clay'
| (balls) -- that had attraction rules that werent meant to
| merge Nurbe surfaces, but rather it would know the
| attractions of various proteins/molocules/biochemicals such
| that it will know which 'covalant bonds' (I am puling that
| phrase out of my non-chem butt) -- work together.
| zeagle wrote:
| Cool tool!
|
| It brings back memories: one of my favourite high level
| undergraduate course finals involved being given some
| instructions, printouts of sequence/primers/enzymes cleavage
| sites/other plasmids and a rough list of my resources and told to
| make a specific product. The exam was long answer essay writing
| out step by step instructions with rationale.
|
| I did the whole thing and double checking realized I misread an
| initial sequence in the first few steps making the whole thing
| void and probably more or less difficult than intended. I added
| an oh shit disclaimer in my solution. The prof, a researcher, to
| his immense credit presumably took off some points but the point
| of the exercise was testing a skillset and I did excellent in the
| course. Basically how higher education should be and night and
| day difference from 1000/2000 level courses!
| dekhn wrote:
| In college, I took one lab course different from all the others
| after a senior told me it was life changing.
|
| In this lab the class was broken into teams and you were handed
| a smelly pile of bacteria. You were told the species and then
| had to read the literature, to learn how to purify specific
| restriction endonuclease (an enzyme that cuts DNA at a specific
| location based on its sequence). You were given access to basic
| molecular biology lab equipment. At the end, each group shared
| its RE and everybody used everybody's RE to map a plasmid. This
| is 1970s state of the art, but by the 90s was pretty much
| routine.
|
| The class kicked my ass. I struggled at every step and barely
| managed to reach the end. Lab work is quite hard and it can be
| challenging to master the techniques. A coworker was moved to
| tears during a challenging step involving a purification using
| a membrane bag, but reasoned that since tears are salty, they
| probably helped the purification when they landed in the
| solvent.
|
| I passed, but barely, and it took me ages to learn even the
| basics of doing stuff in the lb. it's one of the things that
| convinced me robots will do a better job in the lab than any
| human, although in retrospect, it's actually quite hard to
| build a robot that's better than an average lab tech.
| colechristensen wrote:
| I had a few professors who would actually give full points in
| these situations because knowing that you're wrong is often way
| more important than being right. If you went through a process
| mostly correctly and then identified that you were wrong and
| explained it well enough you got nothing taken away.
| plascad_toss wrote:
| This is cool! I've worked on a tool like this for a major
| biotech, its nice to see an open source version with a decent
| feature set.
|
| Looks like your other work is related to UAVs. How did you find
| this problem space? What was the inspiration for this tool?
| devdao wrote:
| Exciting!
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