Fair and Square
Pretty easy to pass the qualifier, I did the first problem – Tic-Tac-Toe-Tomek -. I did the small and large inputs, so I guess that alone would qualify me because it’s 10 and 30 points; and all you need is 35 I think. But who knows, maybe I made a mistake with the large input (which doesn’t get checked until [...]
Google Code Jam 2013 Qualification Ro...
Fair and Square
Pretty easy to pass the qualifier, I did the first problem – Tic-Tac-Toe-Tomek -. I did the small and large inputs, so I guess that alone would qualify me because it’s 10 and 30 points; and all you need is 35 I think. But who knows, maybe I made a mistake with the large input (which doesn’t get checked until [...]
Our (short sale) Home Buying Timeline
Just thought I’d post this up, since I was always wondering/searching the internet for timelines and things that were/weren’t normal. Who knows if our experiences were actually normal, but here is what it was:
OUR FIRST HOME
~10/19/2012 – Decided to start actually going to look at houses, so that we could get a feel for what [...]
gpodder Error Fix/Workaround: Runtime...
This error has vexed me for awhile now.
Bug 1489 on their site. https://bugs.gpodder.org/show_bug.cgi?id=1489
One fix I was using for awhile was to reboot in safe mode and run gpodder to update my podcasts
Luckily someone came up with a way to get gpodder to run from the command line after resetting the PATH.
I’ [...]
Demand Congressional Term Limits?
I don’t buy the arguments against congressional term limits.
The big one is that if representatives know they don’t need to get re-elected then they won’t care about what their voters think and thus will not represent their electorate…
umm, they don’t currently care a great deal about their electorate except fo [...]
A better economy, some steps to take ...
Stop helping already!?
This, seemingly endless, bad economy and do-nothing government is really starting to wear on me. Lucky for me and my family, we are doing okay. I have been thinking a lot lately about ‘producing jobs’. I found a great job, after a long and aggressive hunt – and I have a lot of degrees and experience, w [...]
In your face Bozo Sort!
FINALLY!
I have been so busy with family, the Phd, research, new job (learning to be a real developer instead of a neuroscientist who plays with computers) – geesh, …I would solve Project Euler problems, for fun, when I had time. And of course, there were tough ones (and a few I still haven’t beaten – dang you Silver [...]
SFN 2012 – NRSF/REST dynamic ra...
Woohoo, I’ll be in New Orleans for the annual Society for Neuroscience Conference (Oct 13-17). My poster is Sunday evening if anyone wants to come talk about NRSF, epigenetics, RNA interference, Bioinformatics,… Electronic lab notebooks .
This might be my last SFN for awhile, as a Bioinformatics Software Developer I’m [...]
Apple’s Death Star
Wow, that’s a whole lot of patent troll ca$h Apple just extracted from Samsung!? Why do people support Apple, when Apple takes from their devotees way too high a profit margin on all their items? It’s some weird form of Stockholm Syndrome where, since you were already leached so much money by this company, you now feel obligated [...]
Boycott Nathans Hot Dog Eating Contes...
TEAM KOBI!
Watching the hot dog eating contest has become somewhat of a tradition for me. It’s just good fun, taken to such a high (absurd) level that you can’t help but to be impressed.
The legend Kobayashi truly raised the level of competition and helped take the eating contest to the masses. Unfortunately, the grinding, powerf [...]
Better Peer-Review,… and less money g...
Now that I’m doing research outside of Academia and don’t rely quite as much on publishing to validate my self-worth J (and secure my family’s future), I thought I would not be so passionate or frustrated with the whole research article publishing process. I am, however, still trying to publish work from my last gig – and I [...]
What the!? “mouse Drag Operation Fail...
ARE YOU KIDDING ME!!??
This took me half a day to fix! So I’m posting it in the hopes that at least one person will find this (and not the countless other useless posts) and be saved from an ever so stupid little glitch that needs a little bit better error message!
I’ll tell you the fix, right up front.
The majority of the fix wa [...]
Google Code Jam 2012 – Round 1B...
Just like last year, I decided to go for the ‘harder’ second question first – with the strategy of getting more points in a shorter time so I could get in the first 1000 and move on. My coding skills are much better this year, I thought, so even though this strategy failed for me last time – I thought it was the way [...]
Google Code Jam 2012 Round 1A –...
Have you ever been part way through typing your password and thought that maybe you messed up?
Is it better to delete and start over or just finish out and hope you didn’t mess up? Are you pretty sure, if you did mess up, it was in the last letter you typed – so maybe deleting one letter and retyping would be best?
Have no fear, i [...]
Google code jam 2012
Well, now that I am a ‘real’ programmer, I thought this would be easy. The qualifying rounds usually are anyway. Unfortunately I just moved and started a new job and have three little boys keeping me busy. Well I only had a little bit of time to put in and I had very little sleep, but I did the first two of four problems and got t [...]
Bioinformatic Software Developer
Well, my family and I traveled a thousand miles to Colorado and I am now (becoming) a Bioinformatic Software Developer at ThermoFisher Scientific. I’m seeing some serious electronic lab notebook stuff – but I don’t think I’m necessarily allowed to talk about their stuff .
I’m drinking from the fire hose of Agil [...]
Annals of Neurology Cover!
Yeah, we got the cover! Granted this particular journal doesn’t have very large images on the cover and they only have a very miniature version of the cover online (so I had to scan it and and put it on my blog for anyone to see it). BUT still, my pretty pictures made the cover
Oh yes, and the research article is good too (p. 4 [...]
The future of electronic lab notebook...
So many tablets coming out!
They are getting better, but they’re not really all that different than the tablets of decades past – However, they certainly are gaining consumer support. I mean, I got one of the $99 HP touchpads in the fire sale. For that price why not. And heck I love the thing (I’ve played with the iPad and m [...]
I’m a Doctor
Yay, I presented my dissertation yesterday (see below). Now I’m a doctor
Shawn dissertation NRSF
Added 08/18/2011: Got 45 minutes? Here’s the video
link
My #WPAppItUp Prototype – STuMP
Here’s my sketchflow quick mock up for a windows phone app (game). Click here.
The idea being direct competition between people for these brain teaser type games and quizzes. Fun and good brain exercise.
I’ll develop it if I win a developer phone
http://windowsteamblog.com/windows_phone/b/wpdev/archive/2011/07/29/mango-device-l [...]
Onenote, Skydrive, Web App, & Gl...
I’ve been running my current lab research project for about 4 years. I started off with a small group and was sharing Onenote 2007 from one computer to two others on our network. I tried a couple times to synch to different cloud services (tried Groove a LONG time ago), but it always seemed easier (and better) to run from a shared comp [...]
Welcome Nathan Patrick 6/1/11 11:11am
Big year for my family! We’re finishing up here at UC Irvine with my PhD, looking for a new job and possibly moving (contact me if you hear of something), and now the family has grown from 4 to 5! Nathan was born June 1st. 3 boys in the family! (Well 4 if you count me). It’s great fun (and sometimes great drama).
Project Euler – Crazy Function
update:
HAHA! Got it!
With some Mathematica help on solving summations. I managed to see the ‘easy’ pattern everyone talks about in the forum that gets unlocked upon solving it! Boy I really over did this one
(4 a^2 (2 + b) + a (b (9 + 5 b – 5 c) – 8 c) -
3 b (2 + b) c + (4 a – 3 c) (-2 + a – Mod[b, a]) M [...]
Ahh, too slow in 1B Google Code Jam &...
Oh man! I had it. If only I was as fast as these guys to the left!
I got short and long for the 1st problem (but almost everyone did).
I was so close to finishing the second one, (I would have had to get the long set as well at that point in the competition to make the top 1000).
Don’t know if I want to try at 2am my time the round 1C [...]
Round 1A – Pseudominion Busted ...
Hmmm… Google code jam really took it to me in Round 1A. I thought I would be clever and use strategy to get into the top 1000.
I knew my strengths and weaknesses.
Weakness- only a month of programming experience and in Python (which doesn’t execute as fast as C++), so speed is not my friend
Strength- problem solving ability
So, a [...]
Google CodeJam 2011 GoroSort!!! 55pts...
GORO!!!
All I had to do was find the number of elements out of place!! I actually thought I tried that! GCJ
Well, I got 3/4 problems correct. On one of them I didn’t get the Long data set because I didn’t realize I could only try once so I had not yet optimized my code (I thought I could gauge how much optimization I would requir [...]
In your face Rummy and Python! :)
This is kind of a random post, but it relates back to a previous post about Academia.
As I am finishing my PhD in July, I’m thinking about the future. I will have a position in my current lab as a Research Associate Specialist III (I think that’s what it’s called?) after I graduate while I look for a job – thank [...]
post-PC era ELNs?
The introduction of the iPad, and now iPad 2, XOOM, Galaxy Tab,… has prompted some in the tech world to believe we are moving into a new post-PC era (I mean the prophet Steve Jobs said so, it must be true). Well, since Apple’s influence is so absurd on many people, whatever Apple says does actually seem to come to pass. So I thoug [...]
Switchover and Update
Welcome to 2011! I’m in the process of a server switchover and website update.
A Sample of Samples (Simple, Clean, E...
Courier e-lab-book!!
An answer to my ELN prayers, check out the breaking story on engadget.
This is small enough for a lab coat pocket, around a pound, accepts pen input – handwriting recognition, I think it integrates with Onenote! What the!? This would be great.
It doesn’t come out until 3Q or 4Q of 2010, but man the future looks bright for ELNs [...]
Sharing printers from 64-bit(or 32-bi...
This is SO ABSURD, but I thought I would put this here so I could personally find it. And hopefully others will be helped by it. The switch-over from 32-bit OS to 64-bit is on. And for the most part it is fine. But WHY sharing a printer is so insanely hard I have no clue!
Here’s what you have to do
1) Share Permissions
>>1. On explorer, [...]
21 CFR part 11 and Onenote
I received the question below about switching to ELNs, rule compliance, and Onenote:
Hi Shawn,
Im a second year graduate student at the University of Pittsburgh. I was looking online for potential ELN options ( I use endnote for other things myself and was infact wondering how useful it would be as an ELN when I found your page). It seems to [...]
What ELN would you recommend?
I recently got the following email:
It seems that you have so many ideas, why you didn’t build your own
system?
I’m a PhD student, what would you recommend me to use as ELN?
THANKS
-hector
I had to laugh a little, because – have you read my ideas? Some of them are crazy dreams! I can’t wait for mind-computer interface devices an [...]
Happy Holidays – The new year...
I personally tried out the technical preview of Office 2010 and Onenote, but now that the Beta is out, I think I’m going to try actually switching my ELN in the lab over.
So hopefully the new year brings some cool new advantages…and not BUGS
Chek this link out for some my Master’s thesis work that was just published.
http [...]
Going to SFN 2009 in Chicago
I will be at the annual society for neuroscience conference (this year in Chicago – hey, it’s better than the Olympics anyway, right?). Come talk to me about electronic lab notebooks or epigenetics or whatever. My poster information is:
The transcriptional repressor NRSF/REST mediates acquired HCN channelopathy in the epileptogen [...]
Office 2010 Review: ELN improvements ...
The Academia Problem – Preventi...
I’ve been hanging out in the ‘Ivory tower’ of Academia for quite some time now. Trying to push my crazy/complicated tech nerd ideas. (These people work out complex signal transduction cascades of chemicals in the neurons of the brain, but writing into a searchable computer notebook is too complicated?)
We know that as tech [...]
My Guide to a 'Nearly Free'...
In progress……
Only 2 Things You’ll Need
Microsoft Onenote
This isn’t really free (well it is for 60 days). However, it came with Microsoft Office (which most people need or get anyway).
Shared folder on desktop PC to hold the ELN Onenote folder
We have a lab NAS (Buffalo Linkstation Pro) that I tried to use for the shared Onenot [...]
Rescentris – CERF ELN Review pe...
Rescentris – CERF ELN Review pending
Wearable Computer – Wearable EL...
I know, I know, I have STILL not redone the ELN guide. But you know how lab researchers get carried away with their experiments – I will get to it soon, we just submitted a paper so I will (hopefully) have some time.
These MIT students developed a wearable computer that actually looks quite functional. Wouldn’t that be great (when [...]
Off topic: Synergy, Live Writer, and ...
Before I finish up my new guide on how I set up my current lab ELN, I wanted to organize things and fix little nuisances.
Synergy
It may be a cheesy business buzzword, but it’s also a simple and wonderful little program. Synergy is a small program that you can install on multiple computers which allows you to use a single keyboa [...]
Time to make a new ELN-guide – ...
I was pleasantly surprised to actually meet a couple people at the SFN 2008 Annual Meeting who wanted to talk about ELNs!
While discussing how I was using my ‘ELN’, it occurred to me that it has been a long time since I have written a ‘guide’. In fact, I came to the website and noticed it’s very difficult to eve [...]
Society for Neuroscience Annual Meeti...
This is a long shot, but if any ELN users out there are going to be in DC in a couple weeks then stop by my poster at the SFN annual meeting held in the Walter E. Washington Convention Center and say hello.
My poster and session is:
Sat, Nov 15, 3:00 – 4:00 PM
33.7/D65 – Activity-Dependent Increase of NRSF / REST levels suppresse [...]
Adapx – Capturx Excel Forms
Capturx(from Adapx) is back in the news (at least back in mine).
If you read my Review of their pen (which I feel could really bridge the traditional and the electronic lab book worlds), then you know my major disappointment was that I did not have the ability to print my own form or protocol and then use the pen to mark it up.
Well [...]
Vision: The Hands Free ELN of the Fut...
Endulge my wild imagination for a moment. I’m going to discuss a possible Super ELN which may seem outrageous, but actually is feasible now!
I have mused of the ‘Legend’ video recording lab safety glasses in the pa [...]
I'm Done With Classes!
Wow-this first year of UC Irvine’s INP (Interdepartmental Neuroscience Program) was pretty intense.
I didn’t expect it to be so difficult. Then again, my wife did have a baby boy right before the program started.
But, I made it through – now all I have is hundreds of years of lab work and my thesis.
NOW, I CAN GET B [...]
Onenote Web Exporter – Full Int...
Check out the new (to me) Onenote web exporter.
I have my full lab notebook here. LINK
This should give a little better feel to people about how Onenote can be used.
Illegal ELNs: not just a problem in s...
See what I did there?!
The subject of illegal aliens is a hot topic around here (in southern California). ELNs, aliens, similar sounds…. Okay, sorry for that.
So… Let’s look at the LEGAL ISSUES INVOLVED WITH ELNs.
I want to begin with a little bit of a rant. I use Microsoft Onenote, it’s free (in the sense th [...]
Taking notes in class
Rebirth!
A New Lab
Fujitsu FMV-U8240
Dimensions = 6.73″ X 5.24″ X 1.26″
This is a little larger than the OQO, but smaller than my X60 Tablet. It shows definite promise as an ELN you can take anywhere. My X60 is definitely ultra portable, however I can’t take it everywhere with me with ease. This Fujitsu also has an Intel processor in it, so it [...]
PPAR Gamma Presentation at Sigma Xi
***EDIT 5/13*** Here’s a link to the slide show with sound and video (the video is a little messed up though) LINK***EDIT 5/13***
Hey my cool video in the presentation didn’t work on this ppt2flash thing?
Hey the sound’s not working either! Argg.
I’ve been pretty busy with stuff (like this) so I haven& [...]
R2-74
Saturday, May 05, 2007
4:14 PM
In Vitro Transcription-Translation
PR15
DNA template from: ?1 5/4 (4?L) – ?7 5/4, pTRI-Xef(1?L), Blank
Transcription Products: T ?1 – T ?7, T ?1+ – T ?7+ (DNA template & XEF template), T XEF, T B
Translation Products:x2
IVT ?1 – IVT ?7,IVT ?1+ – IVT ?7+, IVT XEF, [...]
Prelim Evaluation of Lenovo X60 Table...
After a couple years with the OQO 01+, I stepped up a couple pounds to the Lenovo X60 tablet. Here are my initial impressions of the comparative pros/cons of both. It’s a short list, but in a month or so I’ll be better able to truly compare the two form factors.
OQO 01+
Size – In a cr [...]
PR16
Geneclean II Kit
Tuesday, May 01, 2007
11:37 PM
Purifying DNA from TAE or TBE Agarose Gels
1. Excise DNA band from agarose gel.
2. Determine the weight of the gel slice in micrograms.
3. Determine approximate volume of gel slice (100 mg = 100 ?l).
4. Transfer gel slice to microcentrifuge tube.
5. For TAE gels, add 3 volumes NaI s [...]
Sciscoop.com story
ELN – Electronic Lab Notebooks – They’re here now!
Even before tablet PCs arrived, computers were used to organize data. However, the old paper research notebook has never budged an inch. With the advent of tablet PCs and increasingly better software, soon the paper research notebook may budge (probably only [...]
TOC
Once I get all the research pages published to the site, I will create a flow chart.
Rather than chronological order (as the pages are in the sidebar menu), this will outline the research flow and results with links to the actual pages.
Example
Experiment 10
FSF Cells
Treated(R2-27)
[...]
Links
LINK PPAR Research – Open Access journal
LINK Scientists stalk PPAR-gamma, find novel cancer connection
LINK Research links diabetes drug, multiple sclerosis
LINK VEGETABLES THAT PREVENT MAY ULTIMATELY CURE SOME CANCERS
LINK Pargluva at EMDAC today
LINK Animations at HHMI
LINK Research Channel – Balancing the Fat Equation
Sequences
PPAR? Sequences
PPAR?1
0 – 5′UTR ATG
1800
AY048694
A1-A2-Exons
CCTTTACCTC TGCTGGTGAC AAGAAGGCTG CATTTCTGCA TTCTGCTTAA TTCCCTTTCC TTAGATTTGA AAGAAGCCAA
CACTAAA
CCACAAATAT ACAGCAAGAA GGCCATTTTC TCAAACAAGA GTCAGCCTTT AACA
AAATTACCAT GGTTGACACA GAGATGCCAT TCTGGCCCAC CAACTTTGGG ATCAGCTCCG TGGATCTCTC CGTAATGGAC
GAC [...]
Onenote to WordPress – WebPubli...
Okay, I really want to webpublish my lab notebook on here so people can have an example and see how convenient it is (and so I can pull up the info to show people whenever I want). So I am working on a good way to publish the Onenote Notebook to wordpress or even just to the web.
[...]
Agarose Gels
Should be Media player below






















































































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