A challenging issue in today's visual neuroscience community is to understand the activity of a network of Retinal Ganglion Cells (RGC) jointly with a stimulus. In this spot, we have several mathematical and computational tools which are based on several frameworks (empirical statistics, encoding and decoding, probabilistic modeling).
In the spirit of our ultimate goal (understanding the response/stimulus), we are faced with two problematic questions which are really important (and very correlated) to set a clearer vision and to develop the suitable tools:
1- What framework (and mathematical tools) should we use? Do we build a framework based on all relevant literature works? Are there any guidelines to decide what are the suitable tools?
2- How can we bring a common tool to both biologists (neurobiologists, experimentalists) and programmers (computational neuroscientists, computer scientists)? Clearly, the best tool for a biologist is a graphical user interface (but they will be limited to available tools) and for programmers is an IDE or programming language (but their works will be hardly accessible by biologists). So, is there a way to build a tool that they both use and be flexible with a common vision and two different working textures?
Agree to what Shubham is saying. And one can master both biology and programming depending on how much time you have in hand. I won't do it but rather collaborate as much as possible.
To answer your specific question, have you looked into this?
http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&ved=0CCsQFjAA&url=http%3A%2F%2Fwww.ini.uzh.ch%2Fadmin%2Fextras%2Fdoc_get.php%3Fid%3D41880&ei=yEnvUtOHD-OiyAG3tYGADw&usg=AFQjCNGkFRG6DwHBKjiWQOH9_wPEJQ5gXg&sig2=aODg03H5bkN_S4uL8lgvaQ
Some considerations, suggestions, & thoughts:
First, you may wish to check out the volume Software Tools and Algorithms for Biological Systems (especially if you have access to Springer's online database).
Second, computational biology and computational neuroscience have much in common, and there exist a number of software packages (many are MATLAB packages or otherwise not self-contained). NEURON (if memory serves) is both free and self contained and used in visual neuroscience. NEST (NEural Simulation Tool), PCSIM, SBPOP. BioNetS (Biochemical Network Stochastic Simulator) etc., are among those that require MATLAB or knowledge of (and capacity to use) Python, C++, etc. However, as MATLAB is among the best computational tools in existence and is suited to neuroscience (hence the book "MATLAB for Neuroscientists") as well as it is for engineering, bioinformatics, etc., one should have access to it (through one's research center/lab) anyway.
3) MATLAB is rivaled only perhaps by R in the number of packages, add-ons, scripts, etc., available for free and relevant for modelling, statistical methods, and (for MATLAB) even the code for stimuli presentation in a fMRI trials.
4) Even teaching tools like Albany Medical College's Virtual Brain Model software are useful for communicating between researchers in fields like the neurosciences and other biological fields. Not all tools need be oriented towards research itself, but to establishing the foundations for interdisciplinary approaches, groups, etc.
5) There is perhaps no field in the world in which more complex mathematical methods are used by those who lack even a fairly basic mathematical background than in neuroscience, as many researchers come from backgrounds in the social & behavioral sciences. They are exposed to mathematics through a typically poor introduction to statistics as undergraduates and then take a multivariate statistics course in grad school which would require an understanding of linear algebra and calculus to be useful for more than recognizing that x experimental design corresponds somehow to y statistical method (allowing one to enter data into SPSS and magically get results). The more powerful the software package used in analyses, the more one can misuse them.
6) I would check out the published proceedings from the HCI International conference proceedings, as
a) There is no better example of interdisciplinary approach than these conferences, each of which is actually a combination of an ever-growing number of other conferences (currently, ~12; see http://www.hci-international.org/index.php?module=conference¤t=1&MMN_position=6:6)
b) This is a place where one finds social psychologists, computer scientists, engineers, linguists, etc., coming together to develop (or build upon) frameworks for far more diverse and distinct than that which you refer to.
c) In addition to the volumes published after each conference, the program guides provide information about seminars held such as an introduction to behavioral methods for those coming from e.g., the computer sciences. The names of those who ran these seminars might be useful to you as they have already dealt with the issue to which you refer.
I hope that something in the above ramblings is of at least marginal use.
- Badges
- Science topic
- Similar topics
- Biological Science
- Neuroscience