A recently organized workshop at Pune university virtually invited me to speak about iGEM and synthetic biology. It was an opportunity for me to do something I’ve been meaning to do for a while- have a dialogue with some of my former students who were part of the team. The video of the dialogue is posted here [pune-univ-synthbio].

Timeline of the Local Effect of the Pandemic


The timeline of IISER Pune’s closure is interesting:

  1. 14-March-2020: guidelines from Maharashtra State Govt. to close educational institutes due to high density
  2. 16-March-2020: guidelines from ministry of education (MHRD), GoI, and Dept. of Higher Education GoM to suspend classes till 31-Mar-2020, Labs to be restricted to a bare minimum, hostels to be vacated by 18-Mar-2020, Library shut till further notice, work-from-home advisory to faculty, staff/officers perform functions over internet/email, wellness/security to function
  3. 13-March-2020: possible start of COVID-Testing facility in IISER Pune with volunteers drawn from across PhD and Postdoc research students in biology and chemistry.
1) Indian Scientists Response to COVID-19 (ISRC). Hoax busting, model building, coordinating resources and information for finding a cure, diagnostics and spreading clarity. https://indscicov.in/
2) Johns Hopkins COVID-19 resource center- public health, epidemiology and data.

On synthetic biology


The area of synthetic biology is exploding. Or so it would seem. With Craig Venter, the old hand of genomics now promising everything from bio-energy to solving the climate change crisis, it seems like the solution to the ills of the world. And that ofcourse makes one a little skeptical. To gauge whether this is considered in the community to be overhyped, I thought I’d turn to you the science internet world. If you can click on the options below, I will keep the data and post the survey results. So here goes:

The immediate motivation for this was the SynBio 1.0 meeting recently concluded at Indrashil university, funded by the Dept. of Science and Technology, Govt. of India (SERB). With speakers ranging from the Genomics Czar of India, Dr. Samir Brahmachari doing forecasting of future revolutions in genomics, to metabolic engineering of Tobacco plants from ICGEB Delhi, and an editor from Nature-Springer speaking about predatory journals, it was a rather wide palette.

The most interesting development was to see the enthusiastic students from Jawaharlal Nehru Univ. (JNU) from the 6-month SynthBio training course. These post-grads might become the future trained persons who could be the drivers of new research in India.

On Bacterial Size


Our supporting data relating to the work published by Manasi Gangan and me in Roy. Soc. open science are now available for anybody who wishes to use them at DataDryad

Data from: Threshold effect of growth rate on population variability of Escherichia coli cell lengths

Gangan MS, Athale CA

Date Published: October 10, 2018

DOI: https://doi.org/10.5061/dryad.2bs69.2

Time-lapse images of E. coli MG1655 cells in continuous culture grown in the ‘mother machine’


  • 19-12-2016: Anushree, Kunalika and Manasi’s combined efforts are published in PLOS ONE. A good combination of experiments and computation.
  • 13-12-2016: The lab travels to the MMSYMP: Computational and Experimental Studies of Microtubules and Motors at IIT Bombay, Powai, Mumbai.
  • 21-22 May 2016: Advances in mathematical and computational biology (AMCB) at IIT-Ropar: Instructional school organi

    Logo of IIT Ropar

    IIT Ropar

    zed by the Mohali node of NNMCB (National Network on Mathematical and Computational Biology)- a DST initiative to enhancetraining in math-comp biology. I will be speaking. Visting ਪੰਜਾਬ ਦੇ for science- a first- IIT-Ropar, Punjab

  • The iGEM (international genetically engineered machines) contest for 2016 is accepting PI registrations! Let the games begin!
  • #Biophysics Week called by the Biophysical Society of USA 7-11 March! And some amazing biophysics in the dispersal of fern spores, providing an understanding and inspiration for bio-mimetics.

    A report from the Royal Society Interface 2016 by Llorens et al.

    A report from the Royal Society Interface 2016 by Llorens et al.

  • Reproducibility of measurements in synthetic biology- the 2014-15 iGEM InterLab study involved measurements of fluorescence from promoters distributed to multiple labs have been collated and published in PlosOne. The results suggest measurement methodology is a bigger cause of variation between results from lab-to-lab as compared to the construct themselves. And the IISER Pune team is part of the consortium acknowledged in the paper!
  • Summer-Internship with the most exciting thing in neurobiology DIY since Luigi Galvani’s frog. http://blog.backyardbrains.com/

    Cockroach circadian circuit. http://blog.backyardbrains.com/2015/08/the-roach-race-cockroaches-on-wheels-to-study-circadian-rhythms/

    Cockroach circuit

  • The global availability of scientists and engineers from the World Economic Forum and plotted using Google’s DataViewer
  • 27-30 Dec 2015: the National Meeting on Mathematical and Computational Biology organized by the Pune node.
  • 2015 nobel prize for medicine and physiology- to some

By Jupyter


The Romans are under attack. "By Jupiter"

First steps in installing Jupyter on my Mac OSX 10.12.6 Sierra

  • Getting the Xcode command line tools
  • Install MacPorts https://www.macports.org
  • Install Python 3.5 >>sudo port install python35
  • Install PIP from their site using a curl script to get the most updated version https://pip.pypa.io/en/latest/installing/
  • If you got to this stage then pip should allow Jupiter to be installed. Not yet there.



In 2015 we hosted an iGEM team form IISER Pune. The theme was Mycobacterium revelio- in the spirit of Harry and his revleaing charm. Mycobacterium tuberculosis is prevalent worldwide, but India tops the charts for prevalance. Our project aimed to produce a novel diagnistic tool for low cost and rapid detection.

L to R: Snehal, Ira, Prachiti, Prashant, Yash and Siddhesh.

Follow our updates in our exciting journey here:
Tweets by @Iiserpune_igem

Cycling in Pune


  • Where to buy a ride in Pune

1) Surinder Cycles, Karve road, Deccan (near Garware College)
Road racers (Bianchi, Trek, Cannondale), hybrids (Schwinn, Hercules, Trek), MTBs (Hercules, Schwinn, Trek, etc…. many varieties), standard city bikes (BSA, hercules, hero)
2) Phadke Haud, part of old city has something in the range of 10 shops (hercules company outlet, Sardar cycles with a huge choice, and many smaller ones). Many shops will bargain
3) Life Cycle Mall, Tilak Road (opposite Pandit Automobiles showroom, near Abhinav College intersection, Tilak Road, Pune city)
ONLY high end imported goods. Good cycles and a wide choice, but a tad expensive.

Soon to come: google map links to these places.

Google scripting


Pet physicist


#petphysicist2 is up! Enjoy

#petphysicist1: The first in a series.

Inspired by discussions with experimental biologists, physicists and close friends. None of the characters are meant to harm any person, animal or idea.