Let’s Build Something Together
Latest posts
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Possible new idea with tSNE
Dimensionality reduction is in the hurt of molecular dynamics simulations keeping in mind its importance in reducing the high-dimension data produced during molecular dynamics simulations. It also found application in building Markov State Models and also used as CVs to drive enhanced sampling simulations. Several dimensionality reduction techniques have been used over the years such
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Analysis of MD trajectory using tSNE
Before starting anything with tSNE let’s read what is tSNE and how it has been compared with PCA. You can read it here. Several implementations of t-SNE are available here. A great introductory video on tSNE can be found here. The dataset used in this explanation can be accessed here (named combine_times_ca.dcd and corresponding GRO file
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Jupyter notebook and Matplotlib
I was thinking to use Jupyter notebook for quite a some time and finally I started using it. Here is a quick installation guide for Linux (Ubuntu). If Python is already installed pip3 install –upgrade pip pip3 install jupyter Also you can install it with Anaconda. Details here To run notebook jupyter notebook This will
Learn to Explore
Great scientists, artists, entrepreneurs, sports persons are explorers. Following a path defined by the society and incentive structures kills the explorer mindset. Modern science need true explorers.
Make connections
Technologies are build by people. Bringing together a diverse set of people is necessary for substainable technological advancements. Make sure to build connections with people. It matters.
Biology is fascinating. Understanding biological functions at molecular level has significant implications in human disease. I help understanding molecular basis of biological events using physics-based simulations.
Life in Computational Biology 