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:
- 14-March-2020: guidelines from Maharashtra State Govt. to close educational institutes due to high density
- 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
- 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.
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
Gangan MS, Athale CA
Date Published: October 10, 2018
DOI: https://doi.org/10.5061/dryad.2bs69.2
News
- Check out our “OpenPositions” page- an offer for a computational project paid as Project Assistant for training in Biological Image analysis under a BigData framework. Last date for applications 30/12/2017.
To know more about the larger context, refer to - iGEM2017 team from IISER Pune organizes an IndiaMeetup and we have a special guest from Peshawar (via Skype)!
- Our study on the spatial organization of receptor dimerization dynamics predicts a differential effect of membrane heterogeneity of GPCRs and shows how one of these is likely to depend on actin-corrals. To know more read: Deshpande, S; Pawar, A; Dighe, A; Athale, C. A.; Sengupta, D. (2017) Role of Spatial Inhomogenity in GPCR Dimerisation Predicted by Receptor Association-Diffusion Models. Phys. Biol. Volume 14, Number 3
- Dr. Rahul Somavanshi from Univ. Heidelberg and Dept. of Systems & Synthetic Biology, MPI fuer Terrestrische Mikrobiologie (Terrestrial Microbiology), Marburg, Germany speaks to us on PTS system and a fascinating pairwise-FRET study.
- Work done over the last 3 years on protein membrane receptor diffusion and aggregation dynamics to fit to experimental data has been accepted for publication. In this, we show kinetic rates of protein-association in the membrane can predict whether the mobility will be affected by membrane-ordering. Using two GPCR single-molecule kinetics experiments as a baseline we demonstrate the utility of such a kinetic model. You can read more in Deshpande et al (in press).
- An App called Math: A symposium bringing together snippets of research from physics, chemistry, biology, earth sciences and humanities, to highlight the role of mathematics. The biology talk- “Why we have five fingers on each hand and self organised morphogenesis” which invokes Turing patterns.
- The GatesFoundation has an international (mostly) PhD scholarship to Cambridge university. Useful for students in their final year of Masters degrees.
- Our paper on the study of the effect of growth rate on cell size population distributions is now published in Royal Society Open Science. As an experiment for me, we have also released most of our raw-data in spreadsheet format using Dryad Digital Repository: http://dx.doi.org/10.5061/dryad.2bs69
- 11-13 Feb: Andrzej Jarynowski, a researcher in mathematical epipdemiology based in Krakow, Poland visits the lab. His work is an exciting blend of econo-physics, infectious disease and complex systems.
- Shooting stars Gallery of women scientists in a Royal Society project
- 2017-Jan: At long last our work (Manasi Gangan and me) with bacterial cell sizes is accepted for publication!
- 2016-12-26: Anushree’s work hits the popular press. Our work on development and testing an automated kymography tool has been accepted in PLOS ONE. And now it can also be seen in the popular press- the Pune Mirror’s reporter Priyanka Das has filed a report: “IISER comes up with tech for data accuracy” – Pune Mirror -By Priyanka Das, Pune Mirror | Dec 26, 2016, 02.30 AM IST
- 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
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.
- 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/
- 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
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.
iGEM
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.
Follow our updates in our exciting journey here:
Tweets by @Iiserpune_igem
Cycling in Pune
- Cycling trails in Pune- 4 to 37 km circuits
- 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
- List of spreadsheet formulae on google-drive
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.