Tuesday, January 29, 2013

I think my head is falling off

Yeah, I think my head is falling off and I can't sleep! Motha fucker! Someone help me sleep. I think I am going to start taking medication. I used to not be able to sleep but now I often walk up for hours in the middle of the night.

I spent Saturday recovering from staying up till ~5am on Friday. From drinking not from insomnia, haha.

I spent Sunday learning gnuradio and about RF communication because me and some friends were thinking about competing in the DARPA spectrum challenge ( http://dtsn.darpa.mil/spectrumchallenge/Default.aspx ). I learned alot about one way radio communication and error checking and error correction. I did alot of low level network programming when I wrote IP Sorcery and learned so much about networks and shit when I worked for Motorola's iDEN group in the early 2000s. The internets has much different networking we use TCP/IP for most things but one would think that one way communication protocols would be much better due to lack of interference or data corruption?

Anyways, don't know if I will participate in the challenge. I have learned a whole bunch and it has given me some crazy ideas about using wireless induction in cells. Would be really cool to test if I end up doing my Post Doc with Bozhi Tian.

Made up a figure for my Language analysis paper and started writing it up a bit.

Finished my real paper that we are sending to PNAS and almost finished another one that we are going to send to JACS (just need to do some formatting stuff and grammatical stuff).

I think my biggest problem at the moment is finishing things I have an idea and then immediately start to work on it dropping my other projects. This means that projects tend to not be finished. I need to learn that if I want to start a new project I need to finish an old one first and maybe that will push me to finish more things.

And sleep. Yeah I think sleep will help also.

Been writing and coding to this alot:

Thursday, January 24, 2013

Applying for Post Docs

Applying for Post Docs is strange because one is supposed to take on the whole "Look at me. You want me!" mentality which is kind of awkward and absurd but I guess, needs to be done so people know who they are hiring. I am actually attempting the opposite approach, which is "Hey look at me, I am strange and awkward." haha. It actually takes alot of the pressure off and because I am strange and awkward I don't feel bad about it. I figure people need to know what they are going into with me as much as I do with them. Anyways, on to the story.

So yesterday I sent out a Post Doc email to someone at Haaavaaadd, it was the opposite of professionality but again, that's me.
It went something like this with names and identifying information removed:

Subject: Fun Science == Foo + Josiah

Hey Foo,
Hah, Sorry about the cheesy subject line I was just excited to write you. My name is Josiah Zayner, I am a Ph.D. student in Biochemistry and Molecular Biophysics in Tobin Sosnick’s lab at the University of Chicago and I plan to graduate sometime before the summer. I was wondering if you were looking for Post Docs to work in your lab? Actually, to be honest I have been a fan of your work for a while. I study LOV(Light-Oxygen-Voltage) domains and one of the properties is that upon light absorption there is an intersystem crossing from a singlet state to excited triplet state. I was trying to figure out how to use electrostatic interactions from amino acid substitutions or metal ions to modify the photocycle and read about you using those nano magnetic fields. Thought it was super cool. Then I met Bar at the Photosensory Gordon Conference and I just recently saw X give a talk on his work here at UofC for a faculty interview and! I was talking to Bozhi Tian yesterday(do you know him?) and he said I should definitely email you. I have always been a little intimidated by your lab but have decided that I might as well write you. Honestly, I like how your research combines so much, engineering, programing, biochemistry, biology, physics. That is kind of how I approach my research. I like to find a cool idea and run with it, not limiting myself to specific techniques.
As I mentioned, I work on light activated LOV domains. I have been studying them using lots of spectroscopy (UV, CD, NMR, FTIR) and even more protein engineering and mutational analysis, to determine how the light activation chemistry and thermodynamics work and how to make other proteins light activated. In a relative short period of time I have been able to uncover the mechanisms and chemistry of how LOV domains function and apply this to novel optogenetic tools. My skills however are not limited to Biochemistry and Biophysics, I can program in multiple languages (C, Perl, PHP and smatterings of others including ASM) and for multiple microprocessors including TI and AVR. I am author of IP Sorcery an open source network engineering program of tens of thousands of lines of code written in C and part of a number of Linux distributions. I have autodidactic electrical engineering skills and have experience reverse engineering electronics and have accomplished projects such as building an accelerometer based computer mouse (see http://sosnick.uchicago.edu/people/jz.html or if you're really bored http://zaynertech.blogspot.com) and also inventing a wireless cell density spectrometer that sits in the cell culture. I built a prototype and tried to patent it through UChicago Tech though I was unsuccessful; they said the IP space was too small, HAH. However, the thing I am most proud of is the Chromochord, a biosensor that functions as a musical instrument. The protein functions as a kind of pulse width modulated digital output. Using light one modulates the absorbance of the engineered LOV domain and determines the note played. I recently received $2500 fellowship from the University of Chicago to work on further development of this device. I know lots of this isn't directly related to your work but I guess I am just trying to give you knowledge about my skills and loves and hopefully in the process impress you ever so slightly if I may.
Overall I think we both would gain alot from working together. With my biophysics/biochemistry, engineering and programming skills I imagine we could execute some pretty amazing projects. Attached is my CV with one caveat, I am days? away from submitting another first author paper to PNAS (waiting for a collaborator to send me a supplementary figure AGG!) and a month or two? from submitting two more, one from a collaboration that was just finished when I was a visiting researcher in Amsterdam over the summer and the other, an almost finished manuscript from a project I worked on alone in the lab.

Sorry for the longish email. Josiah Zayner
 Yeah, yeah I know The email is a little over the top. Maybe? I was actually just trying to be honest and myself. The guy on his website portrays himself as this fun guy. This was his response:

Dear Josiah,
    Thank you for your interest in my laboratory.  Unfortunately I do
not have any positions available.  I wish you the best of success in
your search for a research position and in your future research
Best wishes, 
I mean maybe he receives 20 of these emails a day and copies and pastes a response because maybe he doesn't have any more space in his lab. It was just weird to feel like cattle. All I hear from PIs is that they hate when people send them some copy and pasted email for a Post Doc. But when potential Post Docs spend an hour writing you an email (I probably spent 10 minutes figuring out if the subject should be: Fun Science = Foo + Josiah, Fun Science && Foo + Josiah, Fun Science == Foo + Josiah, hahaha) and receive a copy and pasted response of two sentences? what do people expect me to do? Spend even more time on an email I know someone won't read?

It makes one even more jaded about scientists. Not much one can do but keep trying harder. Wheew the good thing is I was going to make the email also be an interactive Perl script, HAHAHA. What a cool email that would have been for such a shitty response.

Monday, January 21, 2013

Using a Radiator to generate electricity

So I little while ago I came up with the idea of connecting a bunch of thermoelectric peltier devices together and putting them on top of a radiator and using it to generate enough electricity that I can plug things into this device.

Pretty simple actually. Find a DC to AC converter, they use these in cars for making 12v DC into 120v AC. So basically now all I need to do is be able to generate 12v DC from these peltier devices.

If you are not familiar with peltier devices, they are actually super cool. They use the Seebeck effect to generate eletricity. Basically it is that when there is a temperature difference charge carriers will diffuse from the hot to the cold and likewise. Using semiconductors if we can make the diffusion of the carriers occur at different rates and gain charge separation we can create a voltage.

So I bought a couple peltier devices from eBay, from China and tested them out just by touching them to the radiator. Now the peltier works by temperature difference I know but it was just tests. I found I could measure about 0.3v DC from a TEC1 12706 without any fans or any help creating a better temperature differential. So if I need 3 units per volt and and 12 volts, that's 36 units at about $3 each which is more than I want to spend. Basically, I am hoping I can create a large enough temperature differential that I can make due with 12 or 20 or something.

I currently have 12x TEC1 12706 and 2x TEC1 12710.
I also bought an emergency thermal blanket so I can just drape something over the radiator.

I tested the peltiers in series and they seem to work fine now I just need to solder them all together and duct tape? them to the blanket. Updates coming soon.

Sunday, January 20, 2013


I haven't been updating much on weekends and not because I haven't been doing much. I guess I am just not motivated enough to post stuff. Also, probably because I am slightly hungover.

I have not been able to sleep well lately so I decided that from now on I am not going to sleep until I am extremely tired. It works kind of well I guess...

Been studying alot about Stochastic equations in game theory and population dynamics. Trying to piece together Modern Game Theory. I am finding too many differential equations mixed with linear algebra and I am just like daahhhh, Why can't we just do simulations?

Oh yeah, when I was talking about units moving in gaussian distributions that is basically diffusion, HAH.

I love diffusion and Maxwell's Ratchet I want to build something based off of diffusion/brownian motion. I want to build a calculator (this is kind of a joke I was just day dreaming today). You have a solution and it contains different sized magnetic particles. That are all connected to an electromagnet. When you try and do a calculation it drops the particles and then allows them to diffuse. Based on the mean squared distance different size beads diffuse over say 1 hour you have your answer. The calculator works by changing the temperature to increase or decrease diffusion rates. Ratios of different sized beads at different distances can be mapped back to an actual integer value. That would be fun to build haha. Then to restart you activate the electromagnet so they all have the same initial start position.

Friday, January 18, 2013

Game Theory

Games of Life are really interesting and very simple but it seems to be a field somewhat lacking. With the computational power and the minds we have today why are people stuck on things such as Conway's Game of Life?

Yesterday, i spent lots of time reading on game theory and thinking of different ways to invite new games. The most cool thought experiment game I found was The Pirate Game . I really like the logic and reasoning behind the results.

Ok so what to do.. I was thinking about applying Statistical Mechanics to decision making processes and seeing how that led to self-organization or equilibrium behaviour. Simulated actions would be described by probability distribution. The problem is I keep thinking that I am just coming back to molecular dynamics.

Strategies is also an interesting part of Game Theory. As in finding optimal strategies for simple games.

I am more inclined towards the simulation part though. I just have not been able to figure out how to distill things down to a simple simulation.

Conway's Game of Life was interesting to people because it only had 4 rules even though they were completely arbitrary:

  1. Any live cell with fewer than two live neighbours dies, as if caused by under-population.
  2. Any live cell with two or three live neighbours lives on to the next generation.
  3. Any live cell with more than three live neighbours dies, as if by overcrowding.
  4. Any dead cell with exactly three live neighbours becomes a live cell, as if by reproduction.
I guess it would be interesting to find out how many rules are needed for self-organization. I guess the problem with these games is that there is really no probabilities or random variables. There are sets of defined variables and that is it.
How much randomness or stochasticity would it take to ruin a self-organized system?
 What does it take for a self-organized system to stay self-organized even with X amount of noise or stochasticity?

I need more time to think and maybe more time to drink. It's Friday and almost time for graduate student seminar. 

Thursday, January 17, 2013

What ISO actually produces in Picture Quality

I finally found it:

For my spectrophotography I wanted to find out what ISO and different values actually mean for picture quality and I found a website that has it!
I am stuck between the Nikon D3200 ~$600 and the Nikon D3100 ~$300. I guess I could test them out and if they don't work well just return them but then I can't buy them off of eBay and eBay saves some money. Well D3100 is like $300 on eBay and about $475 on Amazon! The D3200 is about the same on both unless I troll eBay seriously.

Hmmm tough choice...

A Heated Hoody? Hoodie?

Hoody sounds like a hoodlum but I will go with it.

For Christmas I built my brother a heated hoody it ended up costing around $100 but it is pretty badass.

4x 5x15cm Heating Pad  @ $4.95 = $19.80

1x Wearable Keypad @ $12.95

8x 2500 mAh NiMH Battery - AA @ $2.95 each = $23.60

1x NiMH Battery Charger @ $7.95

2x Battery Holder - 4xAA Square @ $1.95 = $3.90

1x N-Channel MOSFET 60V 30A @ $0.95

1x Arduino off of eBay from China or something @$13

1x Hoody @ $25

I generally prefer buying stuff on eBay or Digikey because the prices are much cheaper than SparkFun but they had that wearable keypad and I wanted shipping in a reasonable amount of time so I went for it. Also could have separated the ATMega from the Arduino and used it as a standalone but didn't feel like spending the time to do that to save $10.

Basically the way the jacket works is that there are two pads in front and two pads in back. The wearable keypad controls the temperature through the PWM output and the MOSFET. The MOSFET is for switching the control voltage/current to the heat pads. This is needed because the Arduino I/O has a 40mA max current and we need alot more, the Heat pads draw ~700mA at 5v.


Arduino code:


I wanted a place to store all my code in an easy readable format so I thought I would checkout out Github... HAH

It is a complex subversioning system that I could fucking care less about. I just want to upload code not add, init, commit. Seriously...

I found this and yeah that is how complicated it is...

Wednesday, January 16, 2013

In Memory of Aaron Swartz I found this on Pastebin



I found this sketchy looking posting:

It has to be some kind of code or somebody who wants to murder someone? Anyways, I was looking for a decent Steganalysis program online, let me rephrase that. I was looking for a functional steganalysis program online and could not find one.

Am I bored enough to write one? Hmmm

Really, the person who is trying to give away expired coffee in their freezer is sketching me out.

Tuesday, January 15, 2013


A friend has queued me in on cellular automata.

I don't like to call them cells because these "cells" can actually represent anything so I guess I will refer to them as "units". The first interesting hurdle I have come to is how do two of these units interact. They have a basic function i.e. moving around an xy plane and then happen to try and occupy a space that either another unit occupies or the same space another unit is trying to occupy at the same time. What to do?

There is a simple answer. The interaction either causes something to happen or it does not. Simple. But the interaction can be slightly more complex than that. Say we are talking about proteins then we can say, the interact either effects the Boltzmann distributed state of the protein or not. How much? Do I really want to give each unit a distribution of states akin to the partition function?

What about ion diffusion? Can I recapitulate ion diffusion to the extent that I can make a self-organizing system? I guess that is basically what molecular dynamics tries to do but I guess I am trying on a simpler level.

I think I need to setup a goal for these units and then give them choices and figure out how simple systems solve problems. How they communicate.. &c.

I know everyone hates Perl but go cry to your mommy here is the basic outline code I am thinking about:


# $grid[256][256];

$grid[0][2] = 5;

print "$grid[0][2]";

for($a = 0;$a < $numcells;$a++)

  $x = int(rand(255));
  $y = int(rand(255));
  $grid[$x][$y] = 1;

for($b = 0;$b < $rounds;)
  for($gridx = 0;$gridx <= 255;$gridx++)
    for($gridy = 0;$gridy <= 255; $gridy++)

      if($grid[$gridx][$gridy] == 1)
        $randx = int(rand(2));
        $randy = int(rand(2));
        $grid[$gridx][$gridy] = 0;

           case 0:
           case 1:
           case 2:

           case 0;
           case 1:
           case 2:

        if($grid[$gridx][$gridy] == 1)
          #what to do if someone is already here?

LEDs and Windows

I just received some LEDs I ordered for eBay and wanted to test them out because the last batched I ordered flashing LEDs by mistake. I didn't have a power source close by besides a microUSB plug connected to my Windows laptop so I connected the LED to the proper pins and it glowed. But then windows freaked out and wouldn't recognize any of my USB devices so I had to restart.

Let this be a lesson.

Cool Picture


Found it from here:

Been on this big dubsteb kick lately while writing papers or coding.

Monday, January 14, 2013


Me trying to order something from Walgreens online. Yes, I shop as much as possible from home, don't hate.
Please wait while we find an agent to assist you...
Hi! My name is Khadija G. How may I help you?
Customer:  When I try to order online it keeps saying "The United States Postal Service indicates your address has an incorrect apartment, suite, or unit number. Please enter it below to continue."
Customer:  no matter what I eneter
Khadija G:  I apologize for the inconvenience! Thank you for choosing Walgreens.com. I will be more than happy to assist you. May I please have the pleasure of knowing who I am chatting with today?
Customer:  Does it matter?
Khadija G:  Yes please I apologize but we do need to get your first and last name please.
Customer:  Clark Kent
Khadija G:  Thank you Clark are you entering the last 4 digits of your zip code?
Customer:  You mean the extended zip code?
Customer:  My zipcode is 60615
Customer:  Well normally I reside in Metropolis New York and Work for the Daily Planet but currently I am in Chicago
Khadija G:  Ok and where do you want the goods to be shipped too please?
Customer:  ********** Apt 3L
Customer:  Chicago, IL 60615
Customer:  but you can't tell anyone my address
Customer:  There is this guy Lex Luther who has been looking for me
Khadija G:  Thank you Clark I promise not to tell anyone. Do you have a Walgreens.com account already?
Customer:  No
Khadija G:  Ok I would recommend opening a Walgreens.com account first this will allow you to enter both of your addresses.
Khadija G:  I can send you the steps to register.
Customer:  That's ok
Customer:  I will do it myself
Customer:  Thanks for the help
Khadija G:  Thank you for chatting and please accept our apology for the inconvenience you experienced.
Customer:  and keeping my identity safe
Khadija G:  I understand Clark.
Customer:  *wink* of course you do. Goodbye.
Khadija G:  Goodbye Clark

Language Analysis

I have been working on a project for a while trying to analyze different modalities of the English language using Google Books, Twitter, IRC Chat and Phone conversations. The project is really quite interesting and has taught me a decent amount about statistics and linguistics. Lately I have been trying to create a confusion matrix with the different corpora in order to determine how different/similar these modalities of language we speak are. I am finally finishing up this project with what I consider respectable data and respectable results.

My goal now is to write up a nice little paper and send it off to some open access journal. I spent lots of yesterday coding and making some figures. I still love Perl despite its faults.

Sunday, January 13, 2013


Stupid Perl.

I think this is the second time I have encountered an error inherent in Perl.
This one has to do with the way Perl handles significant digits for arbitrarily long numbers. I was trying to make sure my confusion matrix program was running by comparing a language corpus against itself and it seemed to be a few numbers off in the matching. Finally I started comparing the actual values and like the 10th significant digit is off. Weird.

This is for my Language analysis project. I will write more on it soon. Now I need to think of a simple way to chop off 10 significant figures.


Friday, January 11, 2013

They trust me

BONUS! Well I guess there is one good thing about pretending to be smart.. people give you money.

I finally received the $2,500 for the Art/Science Fellowship/Fellows/Grant thing I received to work on building the Chromochord and the money is "no strings attached" I am super excited and now can buy lots of stuff.

I am working with a pretty cool composer, Francisco Castillo Trigueros.
Here is some of his music: https://www.youtube.com/watch?v=kZm0l4QDgto


I just thought they were joking when they said the Twinkies would be all gone. Isn't someone supposed to buy Hostess and continue to make Ding Dongs and Twinkies and Cup Cakes? Anyways, I was given a box of Twinkies for my birthday which is coming up. I have been craving them for a bit. I could not find them anywhere! I can't believe the day has come where one cannot just walk into a gas station or grocer and buy some cup cakes or ding dongs. Hopefully someone buys Hostess and continues to make the tasty treats.

Thursday, January 10, 2013


I forgot how much I like the Varian VNMRJ interface. We installed new Bruker consoles in our NMR facility and they are damn fancy there is like a bajillion buttons and stuff. I like VNMRJ because there is not a bajillion buttons in fact I think they opt against buttons. One more HSQC and I have collected all the data for this paper! Well at least until the reviewers respond to us. I pick up my check tomorrow for building a new version of the Chromochord. This means lots of cool science! I am excited and need to figure out what to buy. I was looking at the Nikon D3200 if I end up doing the Spectrophotography which I think at the moment is the best way to go. Life is good when you have money to spend on cool science toys. Going to do the elliptical today at the gym. I actually kind of enjoy it. I don't really enjoy running even though I play so much soccer.

Tuesday, January 8, 2013

My New Model of Protein Function

This is an email i sent out earlier. I thought it was interesting enough to post here. The residues and secondary structure elements are referenced from the protein I study Avena sativa LOV2.
I think from our study and logically what appears to be a good model of protein function is one in which every residue is important in a context dependent manner. What this means is that one can mutate a residue but the protein can make up for it by certain residues having a new function or a new chi angle or something. If we mutate out one proposed pathway in our protein another can take over. Maybe the protein went through this transformation during evolution in the reverse. Maybe the beta sheets at one time were the only way to signal the Jalpha helix and then the A'a helix evolved to control the Jalpha because it is more energetically favourable than the beta sheets. The beta sheet function is still under slight selective pressure so it sticks around. Now if I disrupted the A'a helix the beta sheet function can take over. Imagine this on a smaller scale with residues. If I make L408A mutation and it removes the interaction between the A'a helix and Jalpha helix that is bad but maybe T407 forms a previously not found interaction due to the new phi/psi/chi angle it adopts and it appears from our mutation that L408A does nothing. The model is that every residue in a protein is context dependent but they all function in a thermodynamic way to give a protein it's structure and function. In one protein we might mutate a residue on the surface and nothing happens because other residues can easily make up for any loss of conformational energy or function. Maybe in another protein the residues can't. However, both residues could effectively have the same role. If I lose my pinky it would suck but my hand could compensate for it. If I lose my thumb it will definitely be a lot more difficult to make up for but both technically play a similar role.

Monday, January 7, 2013



I have a couple cool things to post on I just need to post the pictures and stuff!

Purifying my last protein for my paper today, woohoo! Only 107 constructs!

Sold a HeNe laser on eBay. I bought 27 of them for $107, crazy deal. Been playing around with them a little bit. Most I have tested are Red. No idea what to do with them yet or if I should just sell them all and make a bunch of money. I sold that one for $25. Yep, one of them for $25, hah.

 Sending some a plasmid containing Taq polymerase to a guy in Estonia for DIYBio.

Have a meeting for the Art/Science Fellow thing tonight. Get to drink wine and act like a fool. I am pretty good at that. Glad we already have a prototype for our project! The Chromochord. BOOM!

 Worked a little this weekend on the Spectrograph Camera I am really having a hard time wrapping my head around what wavelength of light determines a "color" or really if there even is any such thing as a "color". I didn't think this would be so much brain effort.

Friday, January 4, 2013

Programming Languages

I was looking at the job requirements for some of the jobs at Dwave, the quantum computing company. For a software engineer they want someone that has experience with C and Python. Does that exist? I thought those things were mutually exclusive. Besides that fact they have the typically computer/hardware/software engineer requirements, i.e. we only want people skilled in every platform and every language in existence. haha, I thought people stopped asking for that.

Be able to write device drivers for Linux, check, Windows? WTF?
Experience with internet protocols, check, and RS485? WTF?

Don't worry I am not applying I just thought the requirements are kind of _out_ there.


I spent like 6 hours last night trying to get my Kinect to work in Linux it seemed so easy from the OpenCV website. I should have known better. I actually got the Kinect video working the problem was with the body and skeleton tracking functions which are part of NiTE. When I downloaded the latest version of NiTE 2.0 there didn't seem to be any files in the download or rather the correct files! WTF! I didn't want to install an old version of NiTE for fear that it would break my installations of OpenNi. Dahhh!

We will see how much more effort I put into that.

I need to express my last protein today before I submit this paper we have been sitting on forever.

I fixed a Fluorescence plate reader the other day, it had a bad power supply need to figure out what to do with it.

I need to find a decent camera for my spectrography project and wait till my money arrives from this Fellowship/Grant thing. Until then I need to find another project.

Thursday, January 3, 2013


Was in early today. Just relaxing a little bit figuring out what I am going to do today.

Been looking for a nice low power mini PC that can run Linux that I can use for Robotics and I think the Beagleboard XM is the best thing out there at moment. I think the main problem is that I don't want to spend 87625171651276 hours just trying to install Linux so I can run OpenCV and bullshit. Raspberry pi is backordered like hell and in all reality is really slow and doesn't seem to be able to compete with the Beagleboard. The Beagleboard xM is however over $100 but you get what you pay for. It also has really nice Linux support and alot of developers. It has plenty of GPIO pins. I think it should work out great.

I think the current problem with technology when developing something is that lots of it needs to be done for scratch. yeah it would be great to use an Android phone but you basically have to port a whole operating system first. I probably spend most of my time searching for the proper tools to build what I want to build than in actually building it!

I used to like to build things from scratch like when I wrote IP Sorcery and refused to use libnet. It could have made things alot easier but I wanted more control and to learn how to code better. If I had to do it again I probably would have coded it the same way but nowadays I think alot more about how not to waste my time on stuff I can just spend $50 on.

Wednesday, January 2, 2013


Found a Monochromator in the lab. Tested it and it works great with something to narrow the slit width. Now all I need is a new camera and a way to pipe the light into the UV spec so I can measure light intensities coming from the monochromator. Lunch time, left over Chinese take-out. Yum.


I forgot about the spectral response curves of the webcam/camera. This is really insane. haha. I thought it would be some simple project and now it is turning into something crazy. These people use a monochromator to create a spectral response curve. They do a really nice job even taking into account the efficiency of the monochromator. http://www.maxmax.com/spectral_response.htm I have a UV-vis in my lab but this means I would need to acquire a monochromator. That means spending money. I will need to think about this a bit before I continue on.

Coffee was good this morning.
My lab bench is a mess.
Will probably go climbing tonight.

Tuesday, January 1, 2013

Interesting problem

So the color that is actually detected by a camera is not absorbance as we usually detect using a spectrophotometer, it is reflectance. Such as Red light being the reflection of Red and the absorbance of Blue and Green. This is going to make this project that much more interesting. I took some spectra today and also some webcam pictures. I am going to try and deconvolute them later and see what I can get. I plan on using OpenCV library with C to analyze the pictures. I am not that big on colors and image processing so I need to learn alot. So many things effect camera images such as lighting, shadows, resolution it is going to be very difficult and interesting. Only half purified my proteins and instead spent lots of time to find decent webcam software for Linux. I think I will also mess around with Blender a little bit tonight if I can make it work. Just because it seems like a cool program but also because I want to be able to use it for 3D printing. Maybe I should find something easier? Chinese take-out for dinner sounds good.

Camera Spectroscopy

Today I am going to work a bit on converting RGB values to spectra. I am going to take pictures of solutions and UV-Vis spectra of them and see if I can create any equations to deconvolute the camera images into the UV-vis. I also need to purify a couple proteins for a paper I am finishing up. Hopefully I can send it out in the next week or so. I will post later on how the experiments go.