Tool:Open source bioinformatics tools: Blaster, Primer Factory, Labtools

Question

[ete]

Hello!

I would like to advertise my new webpage and software tools (open source): http://www.snowformatics.com/

Blaster - A simple and intuitive multitool for performing some of the most common tasks in nucleotide and protein sequence work.

Primer Factory - A primer design and primer search tool.

Labtools - Common calculations in the lab.

Any feedback, bug reports or features requests are highly appreciated. At the moment, the tools work only with Windows OS, Linux is in progress.

Thanks in advance!

Stefanie

Answer 1

[Ram]

Nice set of tools, Stefanie! The graphic element below the data grid view in primer factory looks really cool!

I'm gonna give you a couple of suggestions almost everyone will agree with: Port your tool to be usable in Linux and OS X as well. The tools look like WinForms and the number of Windows folks in our field is a minority.

Second, if you could also have command line option to run the tools, automation and batch processing would get easier.

Cheers, and all the best!

[ete]

Thanks for your comment and suggestions. Maybe some background information. I am a technician and in my free time I do some programming stuff (hobby). Some time ago, I decided to built a GUI interface for frequently used comment line tools which was more convenient for my colleagues. They prefer to use a graphical interface on Windows. Now I decided to put everything together and make them accessible for others. I totally agree to port the tools to other platforms, as I said Linux is in progress. For Mac OS it is kind of difficult because OSx is not common here and I don't have a OSx device. I might decide one day to invest time and effort, I will see. Since all this is done in my free time, implementing and debugging is a bit slow :-)

I am not sure what you mean by command line option. My tools are based on command line programs and basically just connect them with a user friendly interface.

[Ram]

Ah, so you've wrapped command line tools in a UI - that's great! Point #2 doesn't apply, then. And if the underlying binaries/executables are not yours, then implementing them on other operating systems is quite difficult.

Anything that runs on Linux command line should be easy top modify for OS X, but you can save that implementation for later.

[ete]

Yes, exactly!

@RamRS Where would be the best place for advertising the tools for Linux users? At Biostars?

[Ram]

Biostars is a good place to do that. A blog post on the toolkit will also help your cause.

[ete]

Another question or opinion, would it be acceptable if the user install all library him/herself and run the script via python my_script.py? I am not familiar with packaging on Linux/Mac, perhaps later I will have some time to read into. Would this option be ok for the time being?