- #1

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So I am so beyond stuck and my advisor told me that my progress is very slow. I made a post before about how I'm new to coding and everything, but now I kind of have to forget about the "learning" and make progress.

Does anyone have tips on understanding the Baum-Welch algorithm, forward-backward algorithm, and how to translate all of this into code? I found a really good lecture from Stanford's website (https://web.stanford.edu/~jurafsky/slp3/8.pdf [Broken]) and I understand the examples. I just have no clue how to translate this into code.

https://www.ph.tum.de/academics/org/labs/fopra/docs/userguide-82.en.pdf

"To identify conformational states of the sample we can plot the FRET efficiencies in a histogram. This approach is pictured in figure 6. Moreover, we can determine transition rates by measuring dwell times in the FRET traces. A dwell time is the period of time that a system remains in a given state. The distribution of dwell times is given by the rates of the underlying chemical reaction."

So I have written code that give me FRET traces with respect to time step. I was able to get a plot, and also two additional plot that gave me a histogram of the raw data and idealized data ( this plots only the frequency for the two states).

I have no idea how to write a code that measures how long something stays in one given state. I would then have to plot dwell time versus cumulative frequency and extract the transition rates ( which technically I know the correct value of).

In all honesty, my coding knowledge really is at beginner but the stuff required for this project seems advanced ( at least to me).

Thanks for any tips anyone!

Does anyone have tips on understanding the Baum-Welch algorithm, forward-backward algorithm, and how to translate all of this into code? I found a really good lecture from Stanford's website (https://web.stanford.edu/~jurafsky/slp3/8.pdf [Broken]) and I understand the examples. I just have no clue how to translate this into code.

https://www.ph.tum.de/academics/org/labs/fopra/docs/userguide-82.en.pdf

"To identify conformational states of the sample we can plot the FRET efficiencies in a histogram. This approach is pictured in figure 6. Moreover, we can determine transition rates by measuring dwell times in the FRET traces. A dwell time is the period of time that a system remains in a given state. The distribution of dwell times is given by the rates of the underlying chemical reaction."

So I have written code that give me FRET traces with respect to time step. I was able to get a plot, and also two additional plot that gave me a histogram of the raw data and idealized data ( this plots only the frequency for the two states).

I have no idea how to write a code that measures how long something stays in one given state. I would then have to plot dwell time versus cumulative frequency and extract the transition rates ( which technically I know the correct value of).

In all honesty, my coding knowledge really is at beginner but the stuff required for this project seems advanced ( at least to me).

Thanks for any tips anyone!

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