Gap-free neural circuits
Dec 8, 2012, 11:38a - Science
As I mentioned in a previous post, Tots and I are teaching a class on neural circuits this January during IAP at MIT. IAP is a time where anyone can teach anything they want - I think it's a cool testing ground for classes, and we didn't have anything like it that I remember at Stanford.
I'm excited about ... more »
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neha
- Dec 8, 2012, 11:38a
this is awesome nikhil. i might stop by the first class!
Neural circuits
Nov 21, 2012, 11:33a - Science
Neuroscience, the study of the brain, is absolutely fascinating.
But why choose neuroscience over any other pursuit?
We can try to understand an infinite set of things in our world, from the economic effects of rape to the forces that keep atoms together. But only biology takes a stab at trying to understand the very first thing, *us*. Without us ... more »
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Making DNA look simple (again)
Apr 10, 2012, 6:30p - Science
I recently got sick of doing science. After observing my own productivity and passion for science ebb and flow over the past few years, I've found that I live a roughly 6-month cycle: 6 months of scientific experiments, 6 months of something else (usually programming, often blogging, sometimes installing hardware floors and doing experiments on myself). It seems that when ... more »
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Tron
- Jul 25, 2009, 10:27p
Thank you very much for making this available.
belle
- Aug 5, 2009, 7:16a
this is the best thing since sliced bread!! thank you just saved me thousands of hrs
dude,
- Nov 3, 2009, 6:33p
awesome.
jasonII
- Nov 12, 2009, 8:59a
Thanks, this works great. A few things though. Some of us work on large (18kb) genes. Is there any way to change the scale bar? Also, being able to indicate alternative spice events would be nice.
nikhil
- Nov 18, 2009, 9:29p
Thanks for the request jasonll. I've updated the graphic maker so you can now change the size of the scale bar, to be something more appropriate for your 18kb genes. Not sure what the convention is for indicating alternative splice sites - why not just make 2 separate gene models? I guess if there are several it would be nice to consolidate them into one image. If you have any ideas about what this would look like, lemme know.
nikhil
- Nov 19, 2009, 11:54p
Alan Marnett over at Benchfly.com asked me to write a blog post for them about the Exon-Intron Graphic Maker. It's just like this post, slightly revised. Storing the link here for safekeeping.
http://www.benchfly.com/blog/making-dna-look-simple/
omar
- Nov 29, 2009, 11:07p
dude this has advanced my research significantly
jasonII
- Feb 21, 2010, 8:40a
thanks for the scale bar modification. about the alternative splicing, i suppose it would be helpful if you could color them in. this would also be helpful to mark out certain functional domains easily. three or four colors would be wonderful and spice things up a bit!
siavash
- Apr 4, 2010, 6:10p
hi nikhil,
i also wanted to thank you for making this available. saved me so much time. also wanted to second jasonII's comment about other colors, for marking protein domains, etc.
but its wonderful, thanks a million.
Nick
- Nov 15, 2010, 7:09a
Thank you very much for this. I am an undergraduate doing a genetics research project and this has given me the ability to graphically show exon and intron positions the way I wanted to!
Pascal
- Feb 27, 2012, 7:34a
Great tool. What you also might want to consider is that UTRs can be across more than one exon. I think with the current options it is not possible to do that.
nikhil
- Mar 10, 2012, 7:36a
Pascal, actually I think you can do what you want.
Just like with the protein-coding field, separate exons and introns in the UTR fields with commas, and you'll be all set. That way you can display a single UTR containing multiple exons and introns.
jsto
- May 18, 2012, 1:24a
Thanks a mil nikhil
I wonder if its possible to extend the image to show up and downstream regions?
Pakpour
- May 31, 2012, 12:40p
Thank you thank you thank you so much for sharing this program. You have saved me huge amounts of time and it is such an easy and intuitive program to use!
BMD
- Dec 27, 2012, 12:29a
Hi Nikhil,
Thank you for this awesome tool! I used it to make a figure for my PhD thesis. I couldn't find any other tool that would draw high-res gene structures for me. At first, I was skeptical, because your tool required manual input of the sequences and boundaries, when this information is already available for my genes in GenBank. Also I was worried that the spaces and numbers that were contained in the sequences I pasted would mess things up. But it worked fine and only took a few minutes to copy-paste the sequences and put the commas. The genes I'm working with are monster genes with tons of exons each, and some very long introns, so I'm glad it worked so well. The only thing I would have liked is to have an option to have the exons numbered.
On connectomes and cell lineages
Jun 10, 2011, 6:59p - Science
(If I blog rarely and if my rare posts are only about my worms, then I must simply be obsessed with them. And that's just the way it goes I guess.)
The organism, the biological being, is the most amazing object in all the world. I find it more intriguing than basic physics (which in its own right is pretty ... more »
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Yu-li
- Jun 16, 2011, 10:23a
Hi, your post is quite interesting even though I do not fully understand it.
Here's my thought/question that just passed through my mind.
In case of Homo Sapiens(haha;;), "locked-in syndrom" happens. Even if one can no longer respond to being poked in the back or anywhere he/she still can have consciousness. (It would correspond to activities of other alive neurons though...) Motor neurons might not be an essential part of our consciousness.
So, I wonder if "locked-in syndrom" is possible for the worm. It might be hard to answer, but a necessary condition is signals in the neural network even when all the motor neurons are killed. (Life of the worm should be maintained during the experiment(?). I don't know whether it is possible.)
My thoughts are not very clear, because I do not know much about the language of neural network of the worm.
I just thought your ideas about the consciousness of worm was interesting, and I wish to read more on it. Thanks~
A simple web-app for counting events over time
Nov 16, 2010, 11:01a - Science
I've been trying to count the number of times my little worms (aka C. elegans) chew, so a couple weeks ago I wrote a web-app to help me quantify this a bit more accurately. They chew very fast (3-4 times per second), so I needed something that could keep track of that over time. I also needed something that ... more »
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Gokul Rajan
- Nov 16, 2010, 7:49p
Nice work!!
Serena
- Feb 11, 2011, 10:51p
cool～ and，worms do phototaxis！
Video of real bacterial chemotaxis
Jul 4, 2010, 7:02p - Science
(This is the 4th in a 3-part series on the biology of bacterial chemotaxis. Consider it a video bonus. Parts 1, 2, and 3 are also available.)
I finally found a video of bacteria chemotaxing, and I wanted to share it with you (so I could finally shut up about bacteria by reaching some sort of closure on ... more »
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Here's hoping the bacteria don't crawl off the screen
Apr 12, 2010, 5:13p - Science
(This is the third in a 3-part series on the biology of bacterial chemotaxis. The first post described some basic ideas about biological analysis, and the second post introduced bacteria and their chemotactic behavior. And don't forget the bonus video post.)
Alright, now that the context has been set, I can finally dive into my bacterial chemotaxis simulator, which ... more »
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becca
- Apr 12, 2010, 7:06p
Yay! Es un simulador muy bueno.
Rolf
- Aug 25, 2010, 5:04a
Nice app! I've programmed a very simple optimization algorhitm in Matlab and SciLab based on bacteria behavior.
My bacteria takes a step of constant length in its direction. Then, it compares 'sugar concentration'. If lower, it tumbles, otherwise its orientation stays the same.
Interestingly, this procedure finds the minimum of the Rosenbrock function and other test functions.
Bacteria don't have to be icky
Feb 7, 2010, 10:30a - Science
(This is the second in a 3-post series on biology. The first post gave background on the various levels at which biologists analyze organisms. This post discusses bacteria and an interesting behavior that they have called chemotaxis. The last post will present a web app that's an interactive simulator of this behavior. And don't forget the bonus video post. ... more »
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Ruggero
- Feb 18, 2010, 1:21a
I suppose that tumble probability increases with sugar concentration, so the bacteria spend more time in the area they like most.
nikhil
- Apr 12, 2010, 5:44p
That's an interesting idea which I haven't tried, but the conventional wisdom is actually the opposite. Based on what I've read, it seems that real bacteria actually tumble less when they're moving up a sugar gradient, and tumble more when they're moving down a sugar gradient, though they do adapt and return to a baseline tumbling rate.
It would be interesting to try your idea in the simulator (which I just posted) and see what happens. Unfortunately, there's no easy way to do this in the interface provided, so you'd have to change the javascript to try it out.
A Note about Biology
Dec 25, 2009, 3:11a - Science
(This is the first in a 3-post series on biology. I begin with some background, mostly to provide context for the second post, which is about a behavior in bacteria called chemotaxis. The third post will introduce a web app that simulates bacterial chemotaxis, and will be explained in gratuitous detail. I made it over a year ago, and ... more »
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Ruggero
- Jan 4, 2010, 3:26p
Excellent post.
Biological systems are far more complex than any of the system we've been able to come up with so far.
So far.
There'll be a time when the products of our minds will be more complex and smarter than us all. And probably at that time it won't make much sense anymore to talk about 'products of our minds' and 'us' because they will merge one into the other. If you think more carefully, this actually already happened. Do you wear contact lenses? Do you have a tooth filled? Do you have a hip replacement? Do you know of Oscar Pistorius? Technology is rough, but it's slowly integrating with biology. And not only at the macroscopical level. The most interesting works are in nanotechnolgy, where the distinction between an engineer and a chemist (or a biologist) becomes pretty hard to make.
Biological systems of course are still much smarter than robots. This is partly because biology writes information on DNA (about 3 nm), where current technology only goes down to 32 nm. And partly because we don't know how to handle matter properly yet. What is DNA if not a self-assembly material?
'Cleaner' substrates? There's nothing really clean even in engineering, believe me. 'Simpler' would sound much better.
Is there a basic biological principle we are missing? I don't know. I only know that there's a lot more to know about the language used in nucleic acids. If the principle is there, it has to be written down somewhere.
A question: does a virus chemotax?
nikhil
- Jan 4, 2010, 8:00p
As far as I know, a virus doesn't have any ability to actively move through space. A bacterium, on the other hand, uses flagella as propellers to execute a biased random walk through space. So I guess that a single virus wouldn't be able to chemotax. I haven't really looked into it though, and perhaps the right experiment hasn't even been tried, so I could be wrong.
Sundar
- Jan 10, 2010, 5:44p
Nice post, I do find biology interesting when written this way. I hated it because I did not want any part of dissection and infact, refused to in high school.
PS - engineers do not always deconstruct human made devices, sometimes it is also nature like "Big bang" - unless you are differentiating between engineers and scientists
nikhil
- Jan 15, 2010, 12:44p
yep, i'm distinguishing engineers, who build things, from scientists, who try to understand how non-human-made things (nature, socieities, human minds) might work.
oh how vegetarian of you :)
Visualizing a Worm's Neural Network
Apr 21, 2009, 11:17p - Science
For almost a year and a half, I've been working in Bob Horvitz' lab at MIT studying the nematode C. elegans. A microscopic worm of diminutive proportions (weighing in at only 1 millimeter in length), a single creature is just smaller than the size of an eyelash. These worms have been studied since the 1970s and much is known ... more »
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Sundar
- Apr 22, 2009, 6:31p
Very cool, nice to see you doing great work. thanks for the chrome plug:)
Ruggero
- May 15, 2009, 12:46a
Simply fantastic.
Matej
- Sep 5, 2009, 4:33p
I'm involved in neural networks in computing (artificial NN in chips) and this is very interesting for me.. Nice!
Carlos
- Nov 30, 2009, 4:10a
Excellent iniciative!
Diablo
- Sep 5, 2010, 2:13p
Interesting.
Drew Barfield
- Oct 6, 2010, 2:12p
Awesome. A very useful tool.
Gokul Rajan
- Nov 16, 2010, 7:59p
This is simply fantastic! Now i know how your engineering skills are helping you here! :) great work!
Jason Toy
- Jan 30, 2012, 11:00p
great work
jaronimoe
- Jul 19, 2012, 12:35p
Hey nice work!
Did you by any chance publish an article about this tool of yours at a conference?
I would rather cite an article than a webpage ;)
nikhil
- Jul 21, 2012, 9:31p
Nope, no article yet. It's still a work in progress, and there are a few more features I want to add. I'll post a link here if I publish it in the old-school way.
What's wrong with citing a webpage?
jaronimoe
- Jul 24, 2012, 5:30a
There's nothing wrong with citing a webpage but my university prefers literature citations since articles are reviewed and webpages "grow in the wild" - e.g. anybody could state anything on a webpage.
But since I'm citing a visualization application and not some scientific statements it should be no problem.
Thanks again!
jaronimoe
- Jul 24, 2012, 5:36a
I forgot to ask:
what does the size of the arrow tip represent?
nikhil
- Jul 26, 2012, 8:26a
The size of the arrow is proportional to the number of chemical synapses between two neurons.
Likewise, the size of the orange bar is proportional to the number of gap junctions between the two neurons.
Often we assume that the more synapses that exist between a pair of neurons, the more likely the neurons are functionally connected. But this isn't necessarily the case, just a place to start thinking.
A Reflection
Sep 28, 2008, 3:23p - Science
"I sometimes ask myself, how did it come that I was the one to develop the Theory of Relativity? The reason, I think, is that a normal adult never stops to think abour problems of space and time. These are things which he has thought of as a child. But my intellectual development was retarded, as a result of which ... more »
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omar
- Oct 11, 2008, 9:45a
so was he a genius? did he have 5 wisdom teeth?
Why Study the Brain
Jun 1, 2007, 6:08p - Science
To apply to grad school, I had to write a personal statement that explained why I wanted to study neuroscience and why I would be successful at it. Here's the essay I wrote for my MIT application, way back in December '06.
Reading it again, it seems a bit corny. But I guess these things always do. Especially when you're ... more »
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Anonymous
- Jun 8, 2007, 4:59p
wow
Anonymous
- Jun 12, 2007, 10:59p
like the previous comment said really wow!
Anonymous
- Dec 15, 2007, 6:57a
I can't tell you how much of an impact the last para (especially the second sentence) had on me.
Gokul Rajan
- Nov 13, 2010, 9:05p
Ahh.. its really great to hear that someone can have interest in neurobiology from 11th grade!! When i was in school and used to say that i'm interested in neuroscience, people gave me a very strange look!!!! lol :D But I still took up life sciences...
Then why did you go for engineering??
nikhil
- Nov 15, 2010, 12:33a
i guess i had more passion and energy to learn how to build the things my mind kept imagining, dissatisfied with just letting them stall as ideas. funny thing is, even as i do science now, i'm constantly making minor improvements and writing new software to make the experiments easier, more reliable, and more efficient. so the engineering skills have really come in handy for doing science.
Gokul Rajan
- Nov 15, 2010, 7:05a
yeah.. indeed neuroscience is a lot dependent on technology! we need more advanced and innovative technology to solve the mysteries of the brain!!
Water Crystals
Jan 27, 2007, 1:17a - Science
Science is the most arrogant and the most humble of suitors. Endowed with the audacity to seek Truth yet the humility to prove only falsity, it seeks knowledge as its ultimate goal. Its right has been handcuffed by its left, and together the pair lurch through the world, disposing of the old and selecting of the new. The trail behind ... more »
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omar
- Jan 27, 2007, 5:52p
those are quite beautiful! but the idea that the stimulus is the key independent variable influencing the look is just ridiculous, and you do a good job hitting all the major points.
nikhil i suggest you do a quick read in research experiment literature so you can get down with the terms and better organize what went wrong with the situations you're going to examine.
i feel like this is an exercise you'd give a class that's learning how to do "respectable" research. find everything that's wrong with this method. it seems you've hit on all the major things. i'll just mention two key evaluation criteria often used to evaluate experiments: internal and external validity.
internal validity means that an experiment strongly supports the conclusion that the independent variable (in this case, what the water is "shown") causes the variation in the dependent variable (namely, the patterns that are formed). you point out that they didn't control for other factors, they didn't do any reasonable statistical analysis to show that this is unlikely to be due to chance... there are a bunch of competing hypotheses to explain these patterns, none of which have to do with the specific stimuli.
external validity is usually concerned with possible generalizations and repeatability. of course, as you point out, this experiment has no external validity.
http://en.wikipedia.org/wiki/Internal_Validity
http://en.wikipedia.org/wiki/External_Validity
Justin
- Feb 10, 2007, 10:02a
Thanks for doing this research. This is disappointing and comforting at the same time.
me
- Jul 18, 2007, 1:53p
Thank you for your information. You saved me lots of money from buying that book though it has much advertising in many bookclubs and stores! You help lots of people who are Not scientifically inclined,and also to broaden their inquisitiveness and learning.
carmen
- Jul 28, 2007, 12:28a
I just read the book and was looking on line to find anything or anyone that could articulate for me what I felt when I finished reading his book. Yes they are beautiful pictures and it is a interesting idea but the science they used, or present, leaves one feeling betrayed. Thank you for your insight!
student
- Sep 10, 2007, 7:41p
i think ALLAH is true and you need to enter ISLAM.if you don't belive it you look the AL QURAN water crystals!!!!!!!!
ace
- Oct 5, 2007, 10:23a
yea i agree people
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