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.
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]
Self-Organization in nature
The physics of phyllotaxy by Stephane Douady
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
- Science database listing at the LBNL
- JSTOR: one of the oldest (1995) academic search engines
- Google-Scholar: given google’s age (founded 1998), Scholar is a newcomer (2004) source: Wikipedia
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.
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.
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]
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.
- Nai Talim: One day workshop on alternative methods of university education, Univ. of Mumbai, India
- Sujit Sinha, Azim Premji Univ., India Rethinking Nai Talim: What role can universities play. CED Doccentre
- Teaching in a digital age. https://opentextbc.ca/teachinginadigitalage
- Stepen Downes on MOOCs, Canada https://www.downes.ca/cgi-bin/page.cgi?post=57911
- The original MOOC of 2008 by Dave Cormier, Manager of Web Communication and Innovations at the University of Prince Edward Island, Canada https://learn.canvas.net/courses/4/pages/the-original-moocs
- David Cormier “The MOOC model for digital practise” Canada http://davecormier.com/edblog/wp-content/uploads/MOOC_Final.pdf
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
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
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