Thursday, June 21, 2018

IdentiPy -- A central server solution for proteomics labs?

I'll be honest up front -- I can, in no way, evaluate whether this software works. I'm gonna leave this link here so that maybe people I know who can start a Python script without going to their niece's PDF copy of Python for kids  and staring slack jawed at the screen for an hour before getting distracted can take a look at it -- and I can ask them if it's as smart as it looks!

Here's the paper! 

Okay -- there is a bunch of Python stuff out there. Pythomics (whatsuuuup PandeyLab!?!?) and  Pyteomics and PyProteome and pyMzML and UrsGal (which gets points for 1. combining the most tools and 2. being the least easy to confuse every single time with the every one of the others.)

Okay -- so why post another?

IdentiPyServer is why. IdentiPyServer is designed to be a central lab solution for multiple users-- load it up on some powerful box or server in your lab and then all your users can utilize an easy and customizable webpage interface to load up their runs. It's got some other nice bells and whistles like Autotune which will take a look at the data being uploaded and automatically set the search parameters.

How many times have you had to open your RAW data file because you forgot whether you used the ion trap or Orbitrap for MS/MS on that one weird experiment? You can be forgetful AND lazy and not even check and it should all be just fine.

I'm posting a lot of tools lately -- have I put this thing up here yet?

This paper has something in common with IdentiPy -- in that each one had a word in the article title that I had to look up.

"Extensible" sounds like a real word. It totally is, and it means what it sounds like. Doesn't hurt to check.
"Bifurcated" Absolutely not a word. (It is, I discovered).

Once you get over that hurdle -- this is a really interesting perspective from two sides regarding where we currently are with mass spectrometry software and I highly recommend checking it out.

I've got other tools to discuss as well -- including some we're actively evaluating and comparing. There is some GOOD new stuff out there and in the pipelines, but I think we need to keep in mind that we definitely aren't where we need to be yet and development of new and better software tools for specific applications needs to be a major priority (whaaatttsssuuup grant reviewers!??!?!)

1 comment:

  1. Hi Ben, thank you for featuring IdentiPy Server on your blog!

    I'd like to leave a comment for the readers that if you need any help with setting up the server, you can contact me directly (lev.levitsky at We can also create a test account for you on our own server if you want to play around with it first.

    Best regards,