Sunday, April 26, 2020

SimpliFi! Simple, powerful proteomics data interpretation software!

To start -- SimpliFi is a commercial product and is the property of Protifi. I can't make trademark signs, but both those words have those.

Next, however, this is critically important. Ingenuity Pathways Analysis (also gets a TM) is crazy expensive, and was never ever meant for proteomics data. It shows, and I think it always will. But what else do you do? Holy cow, maybe you SimpliFi!

I saw a demo of this at ASMS last year, but it was an outline. If you caught the day 1 virtual US HUPO talks (which you still can here!) John Wilson gave a talk on this program -- and he undersold it. I've been messing around with a demo of it, and it's a game changer for 2 main reasons

1) It make you think about experimental design. (Something proteomics, as a field, isn't real good at)
2) It puts a lot of power at your fingertips in an intuitive way (except for the exerimental design part)
3) The output is proteomics centric (who makes a list with 2 things?)

You should just ignore me and try out SimpliFi here!

I registered and got a demo code to try it out and the data import is fantastic.

You upload your CSV results from whatever you want. SimpliFi then makes solid guesses about that data you gave it. If it is wrong, simply highlight the columns or rows that are correct.

Have you uploaded data into ShinyApps or into Ingenuity? How much time do you spend going back and reformatting your stupid CSV file so that it will identify your data correctly? 99% of the time you've blocked off for your data interpretation? Oh -- is there an invisible space in your CSV? And is that why the browser window locked up for 3 hours while you thought it was processing?

Not a problem here!

Also -- and I'm scared to hope -- for real -- but SimpliFi allows you to put your data in with the distinct batches your files were in. We're thinking about BATCHES -- IN PROTEOMICS?

(Not the game?)

More on that later when I dig up some data where I can test it, right now I'm messing around with some cool cancer demo data -- and look how beautiful this output is!

Okay -- yes -- if you're an expert with R and or Perseus, maybe you won't find this as impressive as I do, but if you're not an expert in this stuff and you're constantly flabbergasted by requests to interpret the beautiful data you just generated -- this may be what you're looking for.

I think it's still in demo/development phase, and we might find out it costs as much as Ingenuity to use when it comes out, but in just one day of messing around with it with classic NBA games playing in the background here and there (Iverson is under appreciated, btw, Hall of Fame or not.) -- I'd write a justification to trade the two out right now.

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