You get the idea. Anyway, stress and the lying-down position combined with acid reflux resulted in the fiery sensation of heartburn as I lay there pondering what felt like my imminent doom. I couldn’t take it anymore. I got up and left. Yeah, I got to work a little early this morning (way early, actually) but I figure that a little more time (spent relaxing, spent blogging) and perhaps some Tums would help me out a bit. So, here I am. Walking into work today I realized that I didn’t have a lot of pictures documenting my time here. So, in the cover of early darkness, I pranced around the building from room to room snapping pictures of the laboratories. Then I got a cup of coffee, sat on a step, and watched the reflection of the rising sun from building I work in.

Thankfully this is not the building where I attended any of my classes, or the thought of sitting beside it for so long would likely be revolting instead of relaxing. On a separate note, as much as Adobe Photoshop’s PhotoMerge plugin disappoints me (it crashes right in front of me every time I try to create an image larger than 4,000×4,000 pixels) I have to say that it worked nicely in my case. This is my lab desk.

It’s clickable too. Go on, click it! I changed desks a few months ago. I thought it would be cool to have a photo of this so, years down the road, I can look back, remember all of the memories, and probably ask myself “why the heck did I choose the molecular biology and microbiology program?”

Currently, I’m listening to Beethoven - Pathetique - Piano Sonata #8 c minor Op- 13.aac at relatively high volume at my desk since no one is in the laboratory yet. This is one of my favorite songs. I have a copy saved on my website, but it’s kind of hidden and unlabeled so it can’t be found on Google and I can’t get in trouble for it (that’s the plan anyway). If you’d like a copy, you can download it yourself (.aac files are like .mp3 files - they can be played with Winamp or Mplayer but they have better sound quality after extreme compression - this 18 and 1/2 minute song is a little over 3 megabytes). Anyhow, the link is: song4.aac and all I ask of you is that you download the file instead of streaming it directly from the website (it’ll save a little bandwidth). Thanks =o)

With all of the uncertainties already afflicting my thesis process, I didn’t want animal confusion to be a problem. From what I heard, about a dozen diabetic animals (in the age range I wanted most for my experiment) were recently killed. I felt that this process needed to be organized before I could properly come up with a plan, and of course, Python would be involved. I spent the morning downstairs manually inventorying mice. I decided that a location-based system would be the most useful. Each cage got its own line on a sheet of notebook paper (actually more like 8 sheets), and on each line I noted the cage location (in story/row/column coordinates), and information about the 1 or 2 groups of animals housed in the cage (count, sex, and date of birth for each group). After a couple hours sweating beneath my disposable hairnet and lab coat, I completed the downstairs inventory. To the side is a picture I took of myself half way through the monotonous process. (I think blood was about to shoot out of my eyes) Later I ate lunch, then did the upstairs. After I finished, I went home and manually entered this data into the computer (open office spreadsheet -> XLS), so it looked like this:

Then I saved this data as a CSV (comma separated values) file (using either open office or microsoft excel). Note that this is done in such a way that it’s very easy to make modifications to the XLS file to reflect new cages, changing cage locations, or animal death. Anyway, once it was in a CSV format, I wrote a Python script to convert the CSV format to a custom easy-to-analyze format which basically boils down to one line per mouse (not one line per cage). This is the Python script:

f=open("data.csv")
raw=f.readlines()
f.close()
animals=[] # [cage,sex,type,dob,age]
cages=[]
def addAnimals(animal,cage):
        if len(animal[0])==0: return False
        if cage not in cages: cages.append(cage)
        count=int(animal[0])
        if animal[1] == 'm': sex="male"
        else: sex="female"
        strain=animal[2]
        dob=animal[3]
        age=int(round(float(animal[4])))
        animal = [cage,sex,strain,dob,age]
        for i in range(count):
                animals.append(animal)
for i in range(len(raw)):
        line = raw[i].replace('"','').replace('\n',"")
        if "-" in line:
                line = line.split(",")               
                addAnimals(line[3:8],line[14])
                addAnimals(line[8:13],line[14])
f=open("data.txt",'w')
f.write('['+str(animals)+"],["+str(cages)+']')
f.close()

Running this script produced a file with content like this:

[[['d-a1', 'male', 'fvb', '09/26/08', 3], ['d-a2', 'male', 'fvb', '08/12/08', 4], ['d-a2', 'male', 'fvb', '08/12/08', 4], ['d-a3', 'male', 'fvb', '12/24/07', 12], ['d-a3', 'male', 'fvb', '12/24/07', 12], ['d-a4', 'male', 'fvb', '11/16/08', 1], ['d-a4', 'male', 'ove26', '11/16/08', 1], ['d-a4', 'male', 'ove26', '11/16/08', 1], ['d-a4', 'male', 'ove26', '11/16/08', 1], ['d-a5', 'male', 'fvb', '10/26/08', 2], ['d-a5', 'male', 'fvb', '10/26/08', 2],...

From there, I wrote an analysis python script. Should I post it? [thinks about it] Sure why not. A warning though, the code is pretty rough. It works though =o)

import pylab

f=open('data.txt')
animals,cages=eval(f.read())
animals,cages=animals[0],cages[0]
f.close()
print "Processing data for %d animals in %d cages..." % (len(animals),len(cages))

##LIMITS######
sex="male" #'male' or 'female'
strain="ove26"
minage=3
maxage=9
##############

selected=[]

def passIt(animal): #['u-l7', 'male', 'ove26', '10/28/08', 2]
        global selected
        if not animal: #dscription 
                title="Displaing "
                if sex: title = title+sex+" "
                if strain: title = title+strain+" "
                else: title = title+"all "
                title = title + "mice from "
                if minage: title = title+str(minage)+" months to "
                else: title = title+"birth to "
                if maxage: title = title+str(maxage)+" months."
                else: title = title+"death."
                return title
        if sex:
                if not animal[1]==sex: return False
        if strain:
                if not animal[2]==strain: return False
        if minage:
                if animal[4]<minage : return False
        if maxage:
                if animal[4]>maxage: return False
        selected.append(animal)
        return True

def histIt(strain="all",col='k',label=True,limitTest=False,lw=None):
        ages,xs,a=[],[],{}
        for animal in animals:
                if limitTest:
                        col='b'
                        if passIt(animal):
                                ages.append(animal[-1])
                                if not animal[-1] in a: a[animal[-1]]=0
                                a[animal[-1]]=a[animal[-1]]+1
                elif strain in animal or strain == "all":
                        ages.append(animal[-1])
                        if not animal[-1] in a: a[animal[-1]]=0
                        a[animal[-1]]=a[animal[-1]]+1
        for x in range(max(ages)+1):
                xs.append(x-.45)
                if not x in a: a[x]=0
        if not limitTest: 
                pylab.title("Ages of %d (%s) Mice"%(len(ages),strain))
                pylab.xticks(range(1,max(ages)+1))
        if not label: col,lw='0.9',0
        else: pylab.title(passIt(None))
        pylab.bar(xs,a.values(),color=col,lw=lw)
        for x in range(max(ages)+1):
                if label:
                        if a[x]>0: pylab.text(x,a[x]+1,a[x],ha='center')

def showSelected():
        cages={}
        ids=[]
        m,f=0,0
        for animal in selected:
                if animal[1]=="female":f=f+1
                if animal[1]=="male":m=m+1
                if animal[0] not in cages: 
                        cages[animal[0]]=0
                        ids.append(animal[0])
                cages[animal[0]]=cages[animal[0]]+1
        ids.sort()
        x=0
        disp="Total of %d mice (%dm/%df)\n\n"%(m+f,m,f)

        disp=disp+"Animal Cage Locations:\n"
        for cage in ids:
                disp = disp+"%s(%d), "%(cage,cages[cage])
                x=x+1
                if x>7:
                        x=0
                        disp = disp + "\n"
        return disp

def getLimits():
        global sex, strain, minage, maxage
        answer=raw_input("Sex [m,f]:")
        if answer=="": sex = None
        if answer=="m": sex = "male"
        if answer=="f": sex = "female"
        answer=raw_input("Strain [ove26,fvb,gfp]:")
        if answer=="": strain = None
        else: strain=answer
        answer=raw_input("Minimum Age [3]:")
        if answer=="": minage = None
        else: minage=int(answer)
        answer=raw_input("Maximum Age [9]:")
        if answer=="": maxage = None
        else: maxage=int(answer)
        print "\n\n"
        print passIt(None)
        raw_input("\npress ENTER to start")
        return

getLimits()
fig = pylab.figure(figsize=(12,8))
histIt(label=False)
histIt(limitTest=True)
masterAxis = [0,pylab.axis()[1]+1,0,int(pylab.axis()[3]*1.15)]
pylab.axis(masterAxis)
pylab.figtext(.4,.85,showSelected(),va='top')
pylab.show()
#fname=raw_input("Enter a name for this image to save it or press ENTER to quit:")
#if len(fname)>1:
#       pylab.savefig(fname+".png")
#       print "\nsaved as [%s]"%(fname+".png")
#       raw_input("\npress ENTER to exit...")
</minage>

Running this code asks some questions about what type of information I should display. if I have it display all male OVE26 animals (for example) the output looks like this (thanks to matplotlib):

Here the gray bars are the total number of all animals, and the blue bars are the animals I searched for (in this case, all male ove26 animals). Comparing FVB and OVE26 charts, I estimated that we had enough male 4-5 month old OVE26 and FVB animals to make the experiment work (about 12 of each group). Searching for male ove26 mice at least 4 months and no older than 5 months old produces this chart:

See how it lists the location of each of the cages and the number of animals I want from each cage? For example, “d-I2” means that there is a cage downstairs, along row I, in column 2, which contains 1 male OVE26 mouse 4 or 5 months old. Awesome list generation! Thanks Python =oD

But wait, couldn’t I have just gone down and looked for 4-5 month old mice? Yes and no. Yes, it would be easy to find (and mark) these mice, but no because I would not have known to look for them. The goal of yesterday’s little python project was to be able to see at one time everything we have, so I could best determine the criteria of the animals I wanted. Before I made this program, I was planning on comparing mice between 5 and 7 months - something that appears would have been impossible based on the animals we currently have. I can also tell what other experiments I will be able to do in a few months, when some of the mid-age FVB mice will grow older. Additionally, this program is versatile and can be used again and again, for many different projects, with no modification to the code required. Yay Python!

Like I said, the entire night was amazingly entertaining. My only regret is that I didn’t get to take the rest of my family! I thought my dad (not too sure about my mom), and my dad’s parents would have liked it. (My mom’s parents would have liked it too, but they don’t live in town) After I left, I said that I wished I bought all of them tickets (even though they were 20$ a seat - for a movie theater!). Yeah, it was that good. So when I heard that Glenn Beck would be simulcasting another event, I jumped on the chance! “The Christmas Sweater” was the title of this event, and I have to say (without going into too much detail) that it was very disappointing. I guess I was expecting something similar to the previous show - two hours of laughter. This was a stage show, in which Glenn Beck pranced around for two hours narrating and acting out each character of a Christmas story. The story was somewhat emotional (about his parents dying and him running away as a 13 year old), and vaguely reminiscent of his life it seemed. Far from a literary masterpiece, the story (that he wrote) contained the fatal “and I woke up and it was all a dream!” component, which made me regret going at all (and especially insisting that my parents attend!). I actually felt the need to apologize to them in the parking lot on the way to our cars. [Sigh] I considered getting the (newly released) DVD recording of “unelectable” for my dad for Christmas, but being that this event was such a flop (and therefore the connotation of anything Glenn Beck related in my parents’ eyes), I’ll be hunting for a different gift for him this year. Anyway, I need to get some lab work done today. Out.