Story incomplete

Up above burning under the sun
Palmyra wanted to be heard
of all its beautiful rhythms..

So was waiting the Araliya
for a day for its fragrance to spread
and send the message of love.



Fix: Rstudio freeze when loading a file

Fix extracted from the discussion at

I must have messed around too much with RStudio Version 1.0.x in Ubuntu 15.04 , that all of a sudden it started being frozen whenver I try to load  a script, by File-> Open or Ctrl+O. However, I could still open them through the file manager or by double clicking on the file name in the file listing under “Files” at the bottom right corner of RStudio.

The fix was to delete the lockfile corresponding to a deadlock in Qt.

Locate the file location by,

find / -name “QtProject.conf.lock” 2> /dev/null

and remove the file QtProject.conf.lock by rm QtProject.conf.lock

Installing kallisto in Linux

kallisto is  a tool to quantify transcript abundances from RNA-Seq data.

kallisto is available from bioconda.  ( and can be installed by,

conda install -c bioconda kallisto

You need to have conda, the package manager which comes with Anaconda, a programming environment for python and R. If you have Anaconda installed, you may still get an error when executing above command as ‘Error: Missing write permissions in: /home/user/anaconda2’. To resolve this, run the command as

sudo env "PATH=$PATH" conda install -c bioconda kallisto


(Assuming that Anaconda has already been added to the path), if you have root privileges.



සින්ඩරැල්ලාගේ දිනපොතින්


අදහන්න බෑ තවම රැය ගෙවුනේ රජ මැදුරෙ
කුමරියෝ වට කරන් සිනිදු සළු පිළි ඇදන්
අත්වැසුමේ ගෙත්තමින් වැහුනෙ කරගැට දෑතෙ
මග දිගට ගෙවුනු පා බුමුතුරුණු සිප ගත්තෙ

ඒ කාලෙ පුල පුලා රජ මැදුරෙ ඇති කියා
සිතා උන් ඒ සැපත සොය සොයා ඇදුනෙ මම
නතර වී තැනින් තැන රජ සබේ අය මැදින්
යන්න අද මට ලැබුනේ මහා රැජිනක් වගේ

මහ මිදුල පුරාවට සිනා ගී සාගරේ
කාටවත් නොපෙනීම හැංගුනා බොහො කදුළු
දැක්කමුත් ඒ වගක් නොදැක්කා වාගේ
හංගන්න මහ හඩින් හිනැහුනා සමහරූ

එකින් එක හා ගැටී නැගූ හඩ මධු බදුන්
යටින් හද දෙදරවන සුසුම් මට ඇහුනා
දිලෙන ලස්සන අදුන් ලා වර්ණ කෙරූ නෙත්
වල තිබුනු වියළි කම මම හොදින් දුටුවා

ඒ කාලෙ පුල පුලා රජ මැදුරෙ ඇති කියා
සිතා උන් ඒ සැපත සොය සොයා ඇදුනෙ මම
ඔපලූ වට තාප්පය දරන මහ සුසුම් කඳ
හොදටෝම බර වැඩී උඩින් පැන ආවෙ මම

ආයෙත් හෙට…

Ride in the Pražský Semmering in Prague

Prague is a city where time seems to have stood still and being in Prague for 6 days was one of the most memorable events of my life so far.  Prague has a lot to offer for a visitor: the beautiful old town with a history dating back to 900, mesmerizing statues around the city, both in old and new towns, gothic castles, enchanting paintings, splendid Charles bridge, the home of Franz Kafka, the famous Lenin wall and the list goes on. While I was fortunate enough to have a feel of all these, an unforgettable experience in Prague was taking a train ride to the suburbs along Pražský Semmering. A lot of details on previously mentioned attractions in Prague are available on the internet, but Pražský Semmering is a hidden gem.

Pražský Semmering refers to a traditional rail line through Prague and the motor-coach train ride takes you to the outskirts of Prague while offering a beautiful view of the attractions such as Charles bridge and the Prague castle. It was difficult to find where I could hop on to this train, as many locals/foreigners seem to be unaware of this rail. The almost empty carriages were a proof of it. After more than two hours of roaming from one station to another in the city,  and failed attempts to know the details of hop on station, I got lucky at the Hlavní nádraží station.  The motor-coach runs on Saturdays, Sundays and on selective public holidays. The timetable of the train is available at I was elated to know I have made it and was eagerly waiting on the platform for the train to arrive. It was a beauty!

Most of the places in Prague were crowded, during my time of visit (July) and this train ride was serene. A handful of passengers, guard and the driver were there. The city does not expose you much to the beautiful nature of Prague and this motor-coach train takes you through it with a mountainous view. To return to the main station one can take a tram from the stop outside Zličín (the last) station. Since for me it was definitely worth another ride, I spent some time at the last station and took the return ride on the same!

තාරකාවක් කී කතාවක්

අඳුරලූ දිනෙක වට, නෑසු කන් ඇති ලොවක
තනිකමක් හැගි විටෙක 
විවර කර කවුලු පත්
මදෙස නෙත් යොමනු මැන

ඉමක් නැති විශ්වයේ නිමක් නැති තාරුකා
එක්ව මා එක්ක ඒ දිලෙන්නේ නුඹටමයි
නැගෙන තුරු හඳ යළිත්
නුඹට තනි රකින්නයි

සාදයේ සැණකෙලියෙ ඇස් නිලංකාර වන
එලිය යට හිඳින විට මිතුරු කැල වට කරන්
විවර කර කවුලු පත්
මදෙස නෙත් යොමනු මැන

දුරින් මං හිඳින්නම්
පණිවිඩය කියන්නම්
වඩා හොඳ හෙට දිනක් පතා නැගි පැතුම් මල්
දැරූ හිත් මග බලන ඒ උදා හිරු නුඹයි

On attendance to the ISMB/ECCB 2017

Attending the ISMB/ECCB 2017 conference, which was held with full of action at the beautiful city, Prague, Czech Republic was an unforgettable experience. I was there to present an abstract on my work in methods for estimating species diversity from data at the International Society for Computational Biology (ISCB) student council symposium. ISMB/ECCB 2017 is my first time at an international conference dedicated to computational biology.
The student council symposium happened prior to the main conference and was full of interesting talks by students, mainly from the USA and Europe and 2 including me from the land down under were there.
Abstracts of the talks presented at the ISCB student council symposium 2017 are available for a read at
The conference kick-started with an inspirational keynote by Aviv Regev, Broad Institute of MIT and Harvard Cambridge, the United States with the attendance of many researchers, despite the fact the event was held in an evening. One could certainly feel the excitement and inspirational vibes within the room.


Keynote event on 21st evening

Four days full of talks, posters, discussions, meetings, industrial booths, networking and refreshments followed next. ISMB/ECCB 2017 certainly put together a significant amount of researches that are being conducted in different areas of computational biology, separating them into 15 Communities of Special Interest (COSI) s.

Being a part of ISMB/ECCB 2017 is a dream come true. It gave me an opportunity to communicate my work to other researchers and receive their feedback. The event also inspired me to do what I want to do: wander into to the wonders of the unknown, because we are all in it together.