Hopes for the New Year
Here’s the news Labrigger hopes to see in 2011.
New developments with optical indicators
A new, super bright fluorescent protein that blows the doors off of GFP-based proteins.
Bright, far-red dyes with huge 2p cross-sections.
Higher S:N genetically-encoded voltage and calcium sensors.
Better fluorescent dyes for calcium, sodium, and chloride.
I know we’ll see important steps in one or more of these areas.
Technical equipment
Molecular Devices updates the software for their patch clamp amplifiers, and makes the new pCLAMP ABF data file format open source.
Seriously.
High-speed 3D AOD scanning goes mainstream.
It’ll happen. But I’m not sure how much progress we’ll see this year.
Mathworks releases a native version of MATLAB for OSX.
This won’t happen– they’re more likely to abandon OSX altogether– but we can hope. I do all my analysis via Remote Desktop already, but sometimes it’s nice to have it running locally.
Software
Better open source data analysis with Python
Many neuroscientists have been programming different applications in Python: visual stimuli, neuronal models, psychophysics experiments, electrophysiology data acquisition, etc. However, until there is an organized package for programming GUIs, controlling DAQs, and doing data analysis with Python, MATLAB, Igor Pro, and other commercial programs will dominate. Eclipse is a nice package, don’t get me wrong, but it’s not going to get most people to switch from MATLAB or LabView.
Have you seen the package spyder? I haven’t used it for real, but it looks pretty cool. I installed it in ubuntu 10.04. It looks and feels like matlab, but it’s python.
http://packages.python.org/spyder/
A new, super bright fluorescent protein that blows the doors off of GFP-based proteins.
Never going to happen. QY of EGFP is already 0.60 and EC is 61,000.
Rhodamine, a very bright dye, has QY of 0.95 and EC of 120,000.
You aren’t going to get much higher than that on a per chromophore basis and any protein-based chromophore must be environmentally shielded, which takes lots of amino acids.
Michael Lin has the brightest new mutant, don’t remember its stats, its maybe 2x brighter than EGFP. Not published yet.
Bright, far-red dyes with huge 2p cross-sections.
Biology needs more chemists.
Higher S:N genetically-encoded voltage and calcium sensors.
Coming…
Better fluorescent dyes for calcium, sodium, and chloride.
Not much progress has been make here since Tsien’s papers of the mid to late 80s don’t you think? Who knows what invitrogen’s acquisition of molecular probes will do to the development pipeline, if there really is much of one for these modalities.
Thanks for the info, Andrew!
>Biology needs more chemists.
I completely agree. It’s like mathematicians in economics. We keep giving them Nobel prizes, but students still seem reluctant to go on that path.
>Higher S:N genetically-encoded voltage and calcium sensors
I think the hybrid voltage sensing systems (based on DPA) are the best things going right now. Maybe I’m biased. Knopfel has made improvements in trafficking, but the signals remain very small. Still, there are some cool experiments that can be done with them. We just have to work within the limits.
>Who knows what invitrogen’s acquisition of molecular probes will do to the development pipeline
A friend of mine has worked there before and after the acquisition. Invitrogen is a big company that hates having old inventory because it looks bad on their financial reports. So all these niche markets, despite having good margins, are abandoned because the turnover is so slow. There’s an opportunity for mom-and-pop companies here, and some are appearing, but I haven’t seen any prolific developers yet.
On the topic of Matlab on Mac OS X there is an interesting, long running thread on macresearch.org:
http://www.macresearch.org/matlab-and-os-x
Some Mathwork programmers have contributed to the discussion, explaining what they were doing to tackle the problem. So far not to much avail, but if nothing else, the thread offers some technical insight into the problem.
On the topic of open source software,
I have started playing with python after several years of programming everything in Matlab. And the NumPy+SciPy+matplotlib pretty much completely reproduce Matlab’s functionality, with matplotlib being very close to Matlab plotting conventions.
As for the programming environments, there are many different ones:
Spyder, as mentioned previously
Eclipse
Eric
simple IDLE
I think we all got used to the fact that Matlab has sort of everything in one place, but there are three major python distributions, which have a complete package of many many different libraries (probably more than matlab toolboxes):
Enthought Python Distribution
http://www.enthought.com/products/epd.php
Python(x,y)
http://www.pythonxy.com/
and
SAGE
http://www.sagemath.org/
SAGE is particularly interesting as it is heavily math-oriented, combining the functionality of mathematica, maple, matlab, and is really a python. it also allows one to work in a web browser using the concept of notebooks.
I personally feel that it’s very hard to program any big projects in matlab, i am having hard time re-learning the code I wrote in Matlab 6 months ago. Although Matlab is good at vector and matrix operations, it is very bad with memory management, and I remember how i had optimize and clear unused variables all the time. it is also quite slow in many other operations not related to linear algebra. Object oriented programming in Matlab is very difficult and I don’t really know anybody who uses it. GUI in Matlab is also not easy, possibly because of OOP implementation.
While in Python, there is a major move toward Qt-based GUI programming ( in fact Spyder is written in Python using PyQt (Python Qt binding)). Qt-based GUI programming is very easy and powerful, plus it includes excellent extensive documentation. Python documentation is also very good.