Local seminar & workshop series

We will begin a CYTOSIM monthly code meet-up (CM)^2 in the lab. Details on the programme and joining us are here. This is to primarily discuss the c++ code for cytoskeletal simulations [src] originally written by Francois Nedelec while in EMBL Heidelberg, now in Cambridge Univ.

Cytoskeleton and Membrane Affinity Group (CMAG) seminar series in IISER Pune. Frequency: [back soon]

Saturday Meet Programme of Dept. of Microbiology, SP Pune University: Frequency:?

BioModeling (site hasn’t been updated recently), NCL-IISER Pune

Biophysics Paschim: A western India biophysics, physical-biology and structural biology grouping. TIFR-Mumbai, IIT-B, NCL Pune, IISER Pune and ACTREC Tata Cancer, Navi Mumbai. Frequency of meetings: 6 months

Most recently Biophysics Paschim has also emerged as the Student Chapter of the Biophysical Society of USA

Computational Cellular Biophysics (CCB)

Cytosim: A cytoskeleton and molecular motor stochastic mechanics simulation engine.  Developed by Francois Nedelec at EMBL Heidelberg. Further developed in my lab (variants) and now open source on GitHub.

StochSim: A stochastic simulator for bio-molecular interactions based on mass-action with individual particles

Smoldyn: Spatial stochastic molecular interaction simulator with nanometer resolution for cellular processes.

PhET simulations: physical simulations of biological (and chemical and physical processes)- amazing for developing your intuition about concepts you need for biophysics

V-cell: The virtual cell simulation engine with interesting PDE solvers. Developed around 2000′s and still going strong. [Ref: Moraru et al. (2008) The Virtual Cell Modeling and Simulation Software Environment IET Syst Biol]

COPASI: A complex pathway simulator. Created by Pedro Mendes. [Ref.: Hoops et al. (2006) COPASI- A complex pathway simulator Bioinformatics]

Self-Organization in nature

Fibonacci series in plant phyllotaxy

The physics of phyllotaxy by Stephane Douady

Romanesco broccoli with fractal patterns

Romanesco broccoli with fractal patterns: Stephane Douady and his work on patterns in nature.

Biophysics meetings and societies

Biophysics Paschim- an informal meeting of Biophysics Labs in W.India. [bpp6 (2014-Mar)]

Biophysical Society (of America): The premier biophysics organization today with annual conferences, multiple specialized meetings and an active mentorship program

Indian biophysical society: based out of TIFR, Mumbai

Physics of Life: Ann. Monsoon School at NCBS, Bangalore. Supported by the Simon Centre.


Kinesin motility and microtubule polymerisation assay from the Koch Lab (OpenWetware)

Yeast growth protocols from the Haber Lab, Brandeis University.

IISER biology centrifuge instructions

Yeast techniques from the YEN (yeast education network)


Carl Zeiss: a microscopy primer

Molecular Expressions: Microscopy primer and image-gallery from Florida State University and Olympus

MicroscopyU: Nikon’s microscopy teaching pages

Basics in microscopy: Leica’s contribution to microscopy teaching

Bangalore Microscopy Course: Annual course conducted at and by TIFR-NCBS, Bangalore (annual): Next up 15-Sept-2020

Image processing in biology

ImageJ the venerated open source collaboratory tool

Fiji is just imageJ Despite the name, a very good out of the box solution based on ImageJ allowing automatic updating of plugins and the likes.

MATLAB image processing toolbox and particle counting- a startup tutorial by Steve Eddins.

Literature review: Search Egnines

Bio-Experimental Tools

Fluorescence excitation and emission spectra of biologically used dyes

PCR primer design tool on the web Primer3

Primer BLAST from NCBI

OligoCalc: a tool to calculate stability of oligos from template DNA strand

The E. coli MG1665 genome project

A Plasmid Editor (APE) A tool to monkey around with genomes.


Mycoflux: Mycobacterium sp. flux balanace analysis toolbox by Tata Consultancy Services (TCS)


EMBL Heidelberg europe’s flagship molecular biology institute
Health Science and Technology (HST), Harvard-MIT, Boston
BioModels database at the European Bioinformatics Institute (EBI)
Science communication in Angrezi.


Govt. of India, Dept. of Science and Technology (DST) grants, guidelines, submission formats, general info.
Govt. of India, Dept. of Biotechnology (DBT)

Tools to check originality (also called plagiarism checkers)

iThenticate: One of the most “serious” plagiarsm checking tools. Unfortunately definitely paywalled. And proably for the same reason this is one of the best tools- it has access to the databases of 10^5 (0.1 million) publications, i.e. journals, books and other resources like theses etc. This is their own claim and it would be interesting if independent verification were possible. Market-segment “publishers and researchers”.

TurnitIn: A tool from the same stable as iThenticate. Mostly targetted at “admission professionals”. Their own studies on how effective the tool is reported in multiple studies. A careful if independent analysis could be useful for the wider scientific community. Also behind a paywall. But their figures are below.

OAPS (open accesss plagiarism search): The German Science Council’s (Deutsche Forschungs Gemeinschaft DFG) effort at providing public-academics with a non-commercial originality check. Unfortunately since my last check (2015/Apr/18) the search facility has been inactivated.

Scientific programming

Experiments with MATLAB [link]

A good introduction to programming in MATLAB is available from the Mathworks Inc. website.

High performance computing with Mac (Apple) [LINK]

MATLAB troubleshooting installs [weizmann] [mathworks]

LaTex for Biologists (and some BibTex) from Tom Schneider

Teaching in online and hybrid modes- tools for the pandemic

The pandemic has brought forth the need to refine the methods of teaching, delivery and even re-structuring the learning process.  Since massively open online course (MOOCs) have been around for a while, as well as their less interactive predecessor Countrywide Classroom of the university grants commission (UGC) via the education media research centres (EMRC) setup in 1993! There is much hype of MOOCs, esp. in the USA and driven by self-appointed “elite” universities, some self-serving and some downright false. Having said that with the compulsion to teach the impending semester online only in synchronous  and asynchronous modes (hybrid model), here’s a set of links to help navigate tools, ideas and methods.

Computational Cell Biology

Computational Cell Biology, Eds.: C.S Fall, E.S. Marland, J.M. Wagner, J.J. Tyson (2000) Springer Verlag.

International Conference on Computational Cell Biology, @CSHL, USA

Internship & short-term project portals

HEIIN Heidelberg University internship portal for students from India

Workplace Ethics, Legal and Social Implications

IISER Pune Biology Lab Safety and Good Lab Practices [2013][2014]

Prevention of sexual harassment at the place of work- Govt. of India, Ministry of Information Technology (MIT) guidelines

100 reasons to become a scientist- from the Am. Scientist Online

Getting around

Pune: getting there, around and away

Pune municipal bus service PMPL and the city-guide bus- Pune Darshan

INTACH’s Pune heritage walk



Underwater fluorescence detection: FireDive and a basic primer on fluorescence

Hiking around Pune

Trekdi A hiking group that organizes treks mostly in and around Pune region, but also to Himalayan destinations

Trek the sahyadris- some tips to trekking in the western mountains of subcontinental India [himadventures]


Omniglot More languages than you ever thought were possible

South Asian Classic Art

Buddhist relics from Gandhar (Kandahar, modern Afghanistan) at Guimet musuem, The largest collection of Asian art outside Asia. Location: Paris, France.
The Diamond sutra: the oldest known block printed text (with date 11-May 868 CE, and author name; about 587 years before the Gutenberg Bible was first printed: source) in the world. Vajracchedikā-prajāpāramitā-sūtra (perfection of wisdom cutting like diamond ) . Location: British Library, London, United Kingdom

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