Not your usual #science #blog
We’ve always defined ourselves by the ability to overcome the #impossible. And we count these moments, these moments when we dared to aim higher, to break barriers, to reach for the stars, to make the unknown known. We count these moments as our proudest achievements, but we’ve lost all that. And perhaps we’ve just forgotten that, we are still pioneers, and we’ve barely begun, and our greatest accomplishments cannot be behind us, but our destiny lies above us. #interstellar #ernestyalumni November 7, 2014 @ernestyalumni #stem #physics #science #mathematics #math #thorne #einstein

We’ve always defined ourselves by the ability to overcome the #impossible. And we count these moments, these moments when we dared to aim higher, to break barriers, to reach for the stars, to make the unknown known. We count these moments as our proudest achievements, but we’ve lost all that. And perhaps we’ve just forgotten that, we are still pioneers, and we’ve barely begun, and our greatest accomplishments cannot be behind us, but our destiny lies above us. #interstellar #ernestyalumni November 7, 2014 @ernestyalumni #stem #physics #science #mathematics #math #thorne #einstein

We’ve always defined ourselves by the ability to overcome the impossible.
And we count these moments,
these moments when we dared to aim higher, to break barriers, 
to reach for the stars
to make the unknown known.

We count these moments as our proudest achievements, 
but we’ve lost all that.
And perhaps we’ve just forgotten that 
we are still pioneers, 
and we’ve barely begun, and our greatest accomplishments cannot be behind us, but
Our destiny lies above us.

-Interstellar

November 7, 2014

#interstellar #ernestyalumni ernestyalumni ernestyalumni

We’ve always defined ourselves by the ability to overcome the impossible.
And we count these moments,
these moments when we dared to aim higher, to break barriers,
to reach for the stars
to make the unknown known.

We count these moments as our proudest achievements,
but we’ve lost all that.
And perhaps we’ve just forgotten that
we are still pioneers,
and we’ve barely begun, and our greatest accomplishments cannot be behind us, but
Our destiny lies above us.

-Interstellar

November 7, 2014

#interstellar #ernestyalumni ernestyalumni ernestyalumni

If you have any problems with installing Sage Math 6.3 for Mac OSX Mavericks 10.9, or sage manifolds, then I hope this or I could help.

UPDATE : 20140910 I got it to work.

I reinstalled Sage Math 6.3 for Mac OSX Mavericks 10.9 by downloading and opening (i.e. double-clicking the pre-compiled binary) and dragging and dropping it into Applications.

For Mac OSX Mavericks 10.9, I had (re)-installed Sage 6.3 for the Mac OSX-like application e.g. download page for OSX 10.9 http://boxen.math.washington.edu/home/sagemath/sage-mirror//osx/intel/index.html sage-6.3-x86_64-Darwin-OSX_10.9_x86_64.dmg

Then I simply followed the instructions on the webpage for sage manifolds. The terminal commands I used were the following:

cd /Applications/Sage-6.3.app/Contents/Resources/sage
./sage —root
bash sm-install-macos-bsd.sh

That’s it. It was my fault that I have a 10.7 version of sage 6.3 running. Otherwise, for sure, the previous steps work for a Mac OSX Mavericks setup.

Also note that I had Xcode 5.1.1 installed, the latest Command Line Tools installed, and MacPorts installed.

Thanks for all the help guys, and also the suggestions. END UPDATE

I need help installing sage-manifolds 0.5 onto Mac OS X Mavericks, with Sage 6.3 installed from binaries. Thanks

sagemanifolds 0.5 installation troubles (that I’m having) Mac OS X Mavericks setup

sagemanifolds 0.5 installation troubles (that I’m having) Mac OS X Mavericks setup

Here’s what I wrote to the authors of sagemanifolds, Bejger and Gourgoulhon; also if anyone is really interested, I can email you the Terminal Output I had, just leave a message on tumblr with your email:

Hi Bejger and Gourgoulhon,

Thank you for your quick replies!

Yes, I have, in all cases, been typing in the directory where Sage is installed. I check the directory with ./sage -root and pwd
The Terminal Outputs which I will include in this email are long and understandably I wouldn’t expect anyone to read through it, but I’ll copy and paste some snippets from them in this email.

So for instance, I know where the sage math root is this way:
-rw-r—r—@ 1 ernestyeung staff 3630 Sep 8 16:26 sm-install-macos-bsd.sh
Chuns-MacBook-Pro:Downloads ernestyeung$ cd /Applications/Sage-6.3.app/Contents/Resources/sage
Chuns-MacBook-Pro:sage ernestyeung$ pwd
/Applications/Sage-6.3.app/Contents/Resources/sage
Chuns-MacBook-Pro:sage ernestyeung$ ./sage -root
/Applications/Sage-6.3.app/Contents/Resources/sage

In Terminal Saved Output sm2, I try sudo … as well:
Chuns-MacBook-Pro:sage ernestyeung$ sudo bash sm-install-macos-bsd.sh

But essentially I get the same errors during installation, as with simply using bash sm-install-macos-bsd.sh
sdk / -find as 2> /dev/null
as: error: unable to find utility “as”, not a developer tool or in PATH
error: command ‘gcc’ failed with exit status 1

Now in both of these cases, I do this on the install of Sage 6.3 where I just drag the icon into my Application folder (all done in root).

Also, on 2 different Macs, but with Mavericks on both, I have XCode 5 installed, along with the command line tools, and Mac ports for gsed.

I tried a sage install from source, but I’m having trouble there as well (Terminal Saved Output sage1).

Thanks for your time, I don’t have any trouble with sagemanifolds 0.4, so I’ll use that in the mean time, although I appreciate that 0.5 is a major update with your tensor module. There aren’t anything else I could think of to try, so I’m going to have to do other stuff. Thanks again,

-Ernest Yeung.

infiinite3scape:

I think we all have that one person that we never truly get over, that we still think about right before bed every night, or you will always jump at a chance to talk to even though you know you shouldn’t talk to, or the first person you think of whenever you’re drunk.

Thank you for this meetme by the lake

Excerpts from “the book” and Applications of TGIM #1, Time Management

The pdf file is here Applications of TGIM #1 : Time Management, pdf at Google Drive

For those who like watching videos or watching me talk Applications of TGIM : Time Management youtube video

From the pdf file:

What did I do exactly that semester?

This is a small example of my schedule, every Monday, Tuesday, Wednesday, every week for the 12 week semester:

On Monday, I get up at around 5:30 am, brush my teeth, shower, warm up some jambalaya, catch the train from Augsburg by 6:39 am, to arrive at 7:38 am in Munich, so to have enough time to walk to the Math Institute from the train station or Hauptbahnhof, to be seated in time for my String Theory class at 8 am.

String Theory class at 8 am to 10 am.

After String Theory class ends, I head straight to the computer room, saving me time from heading over to the library, and I study; it’s the most quiet place in the building for students without an office as students are using computers.

Algebraic Topology class from 12 pm to 2 pm. Then for 2 hours, I go straight to the computer room and study.

I have TA sessions or what they call Exercise sessions or Tutoring sessions over there at LMU for Differential Geometry from 4 to 6 pm with Dr. James Gray, my favorite instructor who had been at LMU.

6 pm, I walk across the intersection of Theresienstrasse and Barer Strasse to the local, smaller version of a supermarket chain Tengelmann, and I buy whatever salads, vegetables, fruits that were in season and on sale, some yogurt, some cheeses, because I didn’t have a lot or really any money, take them with me, and I’m back in the Math Institute a little before 7 pm; I’m watching everyone, students, instructors, professors, staff, leave the Math Institute and building like clockwork, clocking out for the day, while I find a vacated classroom and commandeer it.

I can snack on the vegetables, fruits, yogurts, cheeses I bought while I had an uninterrupted block of time to study and think, from 7 pm to 1:30 or 2 am. That’s 6 to 7 hours of uninterrupted study and quiet thought. It was the best time of the day for me, as I took in all that I learned that day and made it mine. And it was absolutely necessary for me.

By 1:30 am or 2 am, I am exhausted, tired, and crash out on wherever I can. If I’m lucky, and someone left the faculty lounge open, I’d sneak in and crash on a plush, leather couch. If not, I put together 3 wooden chairs and lay down on it. If it was too cold outside during the winter, I found a kitchen utility closet and slept against the wall.

That semester, I had set my alarm to 5:22 am everyday because that allowed me 8 minutes before the daily university maintenance crew came in punctually like clockwork at 5:30 am, and I vacated. I knew they clean the classrooms first, so I head straight to the bathroom and brush my teeth and wash up. By around 6:15 am, the janitor on the floor would have finished cleaning up the classrooms, normally, and so I’d move back over to an empty classroom to study.

Tengelmann is scheduled to open at 7:00 am, but the delivery trucks for fresh bread and produce are coming in by 6:30 am and the workers are already leaving the automated doors open to let deliveries come in and out of the front by 6:45 am. I sneak in and buy enough fruits and vegetables, especially carrots and tomatoes that I could eat out of my hand and I wouldn’t have to waste time to cut or peel. The young German man delivering fresh baguettes sees me and drops me 3 or 4 in my plastic bag. I buy whatever cheeses and sandwich meats that are on sale. I buy my food for the day, hoping this older, but very pretty, and tanned Croatian brunette is working that day. I try to say something in Croatian, even if it’s just Dobar den. Kako si? Hvala. She’s always smiling and always cheerful.

I’m out of there by 7 am and by 7 am, the computer rooms are open and so I would be in one of the quiet, tucked away computer rooms to study, reviewing the notes and problems I worked out the night before, preparing for the classes ahead, while stuffing my piping hot baguettes with cheeses and cold cuts and making mini sandwiches. There was no one, but the reassuring hum of computers.

It was Tuesday, so I would have Differential Geometry at 10 am to 12 pm. I was in the building and I was on time for class. 12 pm to 2 pm, I was in String Theory tutoring sessions. 2 pm to 4 pm, I had Quantum Electrodynamics.

From 4 pm, I go straight to the computer room to study until 6 pm, when I would head to Tengelmann again to buy enough food and snacks for the night’s uninterrupted study session.

7 pm to 1:30 or 2:00 am, I am inside a vacated classroom I had commandeered, studying.

Keep in mind that officially the Math Institute building closes at 10 pm and the doors are locked, and so I am locked in; that’s why I go to Tengelmann at 6 pm to stock up on everything that I need.

5:22 am, after having passed out, I am up again, washing up in the bathroom, darting back into an empty classroom, then heading to Tengelmann to buy food, hoping it’d be open earlier that normally they would and heading back into the computer room by 7 am.

By 8 am to 10 am, Wednesday, it was String Theory class. 10 am to 2 pm, I had time to study. I would treat myself to lunch at noon, if I had the money, at either the pizza shop or the “Asian” restaurant, Tokami, across the street. The Mensa, what they called the school cafeteria there, was 2 blocks away and I couldn’t afford the time to walk over there and walk back - those minutes could be spent studying, reviewing.

2 pm to 4 pm was Algebraic Topology. 4 pm to 5 pm was the very important Exercise class for Differential Geometry, led by Carlos Ramos-Cuevas. With my classes ending at 5 pm on Wednesday, I had some breathing room. I’d still go to Tengelmann to stock up on fruits, lots of bananas, oranges, apples, things I could eat, without peeling, on the fly, carrots and tomatoes that I could wash in the classroom sink and without peeling, yogurt, whatever was on sale, at 6 pm. I would return back to the Math Institute and study for the night.

So let’s do the math. I have 24 hours in a day. I prioritize my study time, especially that uninterrupted block of studying and quiet thought, because there’s where I made the ideas, concepts, and problems from the lecture and books mine. I get 5 hours of study time during the morning and daytime that is broken up, interrupted and about 6 hours of uninterrupted study time for 11 hours. That leaves me with 13 hours.

I was committed to going to every class, every TA or tutoring session, that semester. Class time was long at LMU. Each day, it takes about 7 hours. That leaves me with 6 hours.

I’ve already cut out lunch, and I save as much time (and money, as an unsponsored Masters student) by going to Tengelmann for food and eating it while studying. Of course I have to wash up and brush my teeth in the university restroom. That is going to leave me only with 4 hours.

And so you could see, I’m talking about giving up stuff. Time management. I knew that if I was to become a scholar, I had to start acting like a scholar. I prioritize, I put study first, my classes first, I was going to make it to every single class and TA session - that winter semester, I can tell myself that I took advantage of every opportunity I was given with the lectures and the tutoring sessions. But that meant that everything else became secondary; and I especially cut out commuting. And sleep. It was knowing what was important and what came first, and all my actions, and all the sacrifices I made, were all directly geared to the primary goal.

The pdf file is here Applications of TGIM #1 : Time Management, pdf at Google Drive

For those who like watching videos or watching me talk Applications of TGIM : Time Management youtube video

laughing-treees:

this is important to remember

laughing-treees:

this is important to remember

To the students going back to school this semester: This is the secret to academic success and this one change I made took me from almost giving up to passing Algebraic Topology, Differential Geometry, Quantum Electrodynamics, and String Theory in 1 semester:
http://youtu.be/xzWTLHVHzBM

Applications of TGIM! I wanted a way to give back, and I show how I went from the principles given in the Thank God It’s Monday videos from Eric Thomas and a number of other success stories I looked up to and went to application. I want to share them with you, with the world, so that someone in his or her life will know it’s possible, and what actions can be taken.

Time management - you can’t waste time, like David Shands, Founder of Sleepis4Suckers says. You can’t waste time! If you are someone who isn’t getting the results you want to get out of school or out of work, maybe you’re failing classes, maybe you’re not passing your classes, then I have to tell you, time management is the single thing that completely changed the results I was getting out of my school semester.

I write about Time Management in this .pdf file and the youtube video I made for it will be up on my youtube account.

Remember, like Eric Thomas says, “Go make the rest of your life, the best of your life!”

My notes while I was reading Morita’s Geometry of Differential Forms is up on my Google Drive. Use in the spirit of the Caltech Honor Code.

Morita’s book is in my opinion the best in the business, from being pedagogically friendly to being elegant in its presentation.

A month ago, I was panicking as I was forgetting a number of things from differential geometry, up to principal bundles, but Morita’s clarity helped alot.

In this update, in particular, the structure constants are calculated for Lie Algebra gl(N,R) explicitly.

latex file also up in my google drive: use in the spirit of the Caltech Honor Code and open-source CC. https://drive.google.com/file/d/0B1H1Ygkr4EWJTkJweEJIYjBGVGc/edit?usp=sharing pdf https://drive.google.com/file/d/0B1H1Ygkr4EWJZVhxUGxzT0ZNTGM/edit?usp=sharing tex

I wanted to post this message to @BerniseAng and Craig Montuori: I hear you about your last post which Craig had shared; I was curious if this could be extended to giving for basic science research because basic science research has no immediate ROI (return on investment), but we wouldn’t be here without electricity and quantum mechanics. Original link: http://mobile.nytimes.com/2013/07/27/opinion/the-charitable-industrial-complex.html?_r=0

What course/book are you currently going through right now? Do you have any particular ongoing projects that you are working on? We seem to both be self-learning Python/Django so it'd be cool to see!

learntocodewithme:

Well … I just got back from vacation yesterday ^-^ so i’ve been a bit lagged …

I’ve not yet dabbled in Django. Right now I am finishing up a Coursera class and going through the Python Codecademy project (about 60-70% complete). 

Where I’m at right now, I’m sort of debating learning Django or switching gears and looking at Ruby on Rails. For my purposes, using ruby on rails to build web apps would be more efficient. The more I learn about Python/Django, I hear it’s a lot easier to get up and going with ruby on rails. And that there’s more resources available - so I hear. 

For the next month my primary goal is finishing my learntocodewith.me site. I am rebuilding it from scratch, and it’s the second site I’ve ever done without using a WP theme. So it’s taking me some time :-/

After that’s checked off the list, I’m going to start looking at django or ruby on rails. 

Which coursera class you working on right now?

This is a clean and elegant python implementation of a Hidden Markov Model, the Bob and Alice example from wikipedia, thanks (and shout outs to!) to Sujit of the Salmon Run blog.

I’ve put it up on my github to make it convenient for everybody to download it and play with it.

https://github.com/ernestyalumni/Examples/blob/2bc33a51f45c739760dc760bec55694980a6ee4b/wikiBAHMM.py

from __future__ import division
import numpy as np
from sklearn import hmm

states = [“Rainy”, “Sunny”]
n_states = len(states)

observations = [“walk”, “shop”, “clean”]
n_observations = len(observations)

start_probability = np.array([0.6, 0.4])

transition_probability = np.array([
[ 0.7, 0.3],
[ 0.4, 0.6]
])

emission_probability = np.array([
[ 0.1, 0.4, 0.5],
[0.6 , 0.3, 0.1]
])

model = hmm.MultinomialHMM(n_components=n_states)
model._set_startprob(start_probability)
model._set_transmat(transition_probability)
model._set_emissionprob(emission_probability)

# predict a sequence of hidden states based on visible states
bob_says = [ 0, 2, 1, 1, 2, 0]
logprob, alice_hears = model.decode(bob_says, algorithm=”viterbi”)
print “Bob says:”, “, “.join(map(lambda x: observations[x], bob_says))
print “Alice hearts:”, “, “.join(map(lambda x: states[x], alice_hears))

PS: in the future, I’m not going to try to do a lot of HTML editing to make my posts “pretty” on tumblr. I’ll put up the links and the code will be there on my github, nicely formatted. Same with my math and physics stuff: I’ll put up both the pdf and latex on my google drive page.

The second answer was what I was looking for, big ups, shout outs to jmontross for his direct contribution, and MaxMackie for his question (because I was wondering the same too)

http://stackoverflow.com/questions/9383014/cant-import-my-own-modules-in-python

exporting path is a good way. Another way is to add a .pth to your site-packages location. On my mac my python keeps site-packages in /Library/Python shown below

/Library/Python/2.7/site-packages I created a file called awesome.pth at /Library/Python/2.7/site-packages/awesome.pth and in the file put the following path that references my awesome modules

/opt/awesome/custom_python_modules

jmontross

I needed this because I was trying out this Hidden Markov Model code implemented in Python:

https://code.google.com/p/hmmpytk/

Very telling is this commentary on Python’s efficiency:

“As one may know, Python scripts aren’t the fastest programs on earth, therefore this toolkit will not be able to compete with the C/C++ implementations of HMM in the aspect of absolute speed. However, due to the self-contained nature (doesn’t depend on external packages), there are many use cases for this.”

Why I stick with Python so much is that it is fun to program in (this is first and foremost for me) and implementation is fast. It’s what people call “developer time.”