Show HN: PlasCAD: Open-source plasmid editor
PlasCAD is a design software for creating and validating plasmids and primers in molecular biology, featuring primer quality control, sequence editing, and support for multiple file formats across various operating systems.
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PlasCAD is a design software tailored for the creation and validation of plasmids and primers, primarily used in molecular biology. It is available for Windows, Linux, and Mac, with installation instructions varying by operating system. Key functionalities include primer quality control, primer generation for specific cloning methods, an interactive sequence viewer and editor, and a circular map display of plasmids. PlasCAD also offers features for dynamic annotation of restriction enzyme sites, PCR product generation, and supports various file formats such as FASTA and GenBank. Additional capabilities include automatic annotation of common features, visualization of amino acid sequences, and assistance in calculating solution volumes. Future developments aim to enhance quality control measures and introduce features for identifying secondary structures. PlasCAD is designed to be a fast, lightweight, and user-friendly tool, providing unique functionalities like automatic primer tuning and a compact file format for DNA sequences.
- PlasCAD is designed for plasmid and primer creation and validation.
- It supports multiple operating systems with specific installation instructions.
- Key features include primer quality control, sequence editing, and dynamic annotations.
- The software supports various file formats for interoperability.
- Future enhancements will focus on quality control and secondary structure identification.
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- Users express excitement about the tool's capabilities and its open-source nature.
- Several commenters share their experiences with similar tools and the challenges they faced in molecular biology.
- There are requests for improved user interface options, such as a light mode and better installation instructions.
- Some users inquire about advanced functionalities, like 3D modeling and protein mapping.
- Overall, there is a desire for more accessible resources and guidance for non-technical users.
14 commentsIt 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!
Looks like your other work is related to UAVs. How did you find this problem space? What was the inspiration for this tool?
A few questions:
Can I make the UI light instead of dark?
The 'simulate PCR' works, but seems to unload the original sequence. Can I get that back? This is a bit unexpected.
Tangentially, glad to see more biotech stuff finally making the front on HN! :D
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?
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.
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