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Showing posts from May, 2014

Can we pat an expat!?

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Let me give a try on this post and share few points how it is to be an Expat. Ah yes, I am a graduate student on an alien land. After draining over an exhaustively exhaustive semester, sustaining the stress of presentation(s), assignment(s), applying for intern position(s), am energy deprived but to say, all that glitters is Not gold . You reach a new land, air, and environment with a time shift of 8-11 hours. Beating away the terrible Jet lag, you disrupt your complete schedule: sleeping, working, eating, cleaning, washing, earning, spending money, behavior, thought process, reaction pattern, having cash as little as nothing in wallet and the critical one Cooking , which definitely one learns once settled down. First few days, mind does not allow you to adjust, you float back to the longest flight journey you have ever had, the layover(s), hastiness to get a boarding ticket, searching the terminal of your flight, worry of luggage, waving off your relatives at the gate of a

How to install TOPCONS on local

TOPCONS is one of the many tools available used for transmembrane prediction in GPCRs. It uses prediction by several other prediction methods (scampi-msa, scampi-seq, prodiv, octopus, and pro) and based on which it, spits out the consensus topology. Length of each predicted transmembrane helix is 21. I have had a tough time installing TOPCONS. It had a huge number of dependencies. I thought sharing and contributing might help someone. Instructions: $ svn ls   https://svn.sbc.su.se/repos/cbr/modhmm-projects/trunk/install_topcons.sh Run the above command to see install_topcons.sh on command prompt. If you do not see, then can be an issue with the SVN version you are using. To download the package mentioned at https://svn.sbc.su.se/repos/cbr/modhmm-projects/trunk/cmdline/ Use: svn co https: Prerequisites for installation: - SVN, bash, Linux environment - NCBI old blast . Old blast has binaries for blastall and formatdb.  Add this into your PATH or