just a quick note — Prof. Frey’s idea from a few years ago, which I hope to get more people thinking about:

AP engineering class, portfolio-based

Advance Placement

to encourage schools to teach engineering skills & give teachers a structure and the professional education to adopt engineering into the school curriculum, we could try to implement an AP Engineering class.

portfolio?

to give it relevance to larger numbers of students, this wouldn’t be purely an abstract class, like AP Physics A/B (which I really liked!), with a theoretical test at the end

but instead, like AP Studio Art, you submit a portfolio of projects you built.

Here are some samples: http://apcentral.collegeboard.com/apc/members/exam/exam_information/220194.html

or the more engaging 2014 version: http://studioartportfolios.collegeboard.org/

(sweet oranges, this is some beautiful metalworking:

http://studioartportfolios.collegeboard.org/work/student-1-3d-concentration/ what was I doing in high school? haha )

scale

What AP Studio Art demonstrates is that you can have people submitting & judging a subjective portfolio at scale nation-wide in a reliable-enough manner for students to receive college credit for it.

Thus, the idea of an AP Engineering class where students submit portfolio work is not so outlandish.

However, of note, number of students who took it:

• 2012, AP Studio Art: 16,188
• 2012, AP Physics B: 80,584

I never took AP Studio Art, so I’m not super familiar with how it’s run. Therefore, I do not know if the lower number of students taking AP Studio Art is due to less student interest (not enough student demand) or scaling problems (such as AP Studio Art being expensive to run as a class).

differences

I suspect that an engineering portfolio should show more teamwork than an AP Studio Art portfolio.

a sign of the times

MIT recently instituted a “Maker Portfolio” section. I have a bit of bleahh feeling with all this “maker” talk (since it has been so commercialized by “maker media”), but here is a picture:

 

side-note

there ought to be an engineering portfolio website… as mentioned in an earlier blog post, most portfolio websites are oriented toward UX/UI/webdesign/photographers

in which i spend way too much time going “what was that one game where you can either fix a pond ecosystem or a toilet?”

i’ve been taking a trip down memory lane (there’s so much future to live, not sure what the point is, but it is kind of fun :] )

Here are some of the games I remember playing (with the help of google. sweet oranges, this took Advanced Googling Skills), along with images / videos / play online / download links

1) Super Solvers: Midnight Rescue!

This was a fun detective game. For some reason, I remember it being in black-and-white… anyway, I remember liking the soundtrack a lot, turns out it’s this super-classy song (skip to 0:58 for the part in the game):

Here’s a video of it:

Read more about it / picture sources:

• http://www.giantbomb.com/super-solvers-midnight-rescue/3030-9077/
• http://www.abandonia.com/en/games/1008/Super+Solvers+-+Midnight+Rescue.html
• Wikipedia

Ooh! I found another version of the game (I never played this) which you can play in your browser at the Internet Archive Software Library:

• https://archive.org/details/msdos_Super_Solvers_OutNumbered_1990

2) Number Munchers

I didn’t remember playing this game, even by the screenshots, until I played some version of it online and heard the music.

• Read more / image source: http://www.giantbomb.com/number-munchers/3030-7138/
• Wikipedia
• Play online (I couldn’t get this one to work :/): https://archive.org/stream/Number_Munchers_v1.2_1986_MECC/Number_Munchers_v1.2_1986_MECC.dsk?module=apple2c&scale=1
• Here’s another online one: http://wallofgame.com/free-online-games/arcade/988/Number_Munchers.html

3) Oregon Trail II

I think I played II, not super sure. Here’s a song:

Here’s a full playlist:

image source: Wikipedia.

Play online: https://archive.org/details/msdos_Oregon_Trail_Deluxe_The_1992

’nuff said.

4) The Amazon Trail

 I remember this one better than Oregon Trail. Whoo! I had fun playing this.

• Read more / image source: http://www.myabandonware.com/game/the-amazon-trail-1mf
• Wikipedia
• Play online: https://archive.org/details/msdos_Amazon_Trail_1993

5) O’Dell Down Under

Fishies and exploring the ocean! I realllly liked this game 😀

Image source:

(video has the original soundtrack :] )

• Wikipedia
• Not available online, sadly, but here’s a possible download link: http://www.old-games.com/download/3331/odell-down-under

6) Treasure MathStorm!

I have super fond memories of this too! 😀 heehee catching elves

(video has the original soundtrack :] )

• Read more / Image source: http://www.old-games.com/download/5809/super-solvers-treasure-mathstorm
• http://www.myabandonware.com/game/treasure-mathstorm-1r6
• http://www.abandonia.com/games/1011/
• Wikipedia
• I couldn’t find a link for playing online, but try the old-games.com link for downloading

7) Math Blaster

 

Possibly the “Episode 1: In Search of Spot” version? I don’t remember being super-entertained by this, but I do remember playing it and enjoying it. Here’s what it sounded / played like as a video:

• http://www.myabandonware.com/game/math-blaster-episode-one-in-search-of-spot-41t
• Wikipedia (also the image source)

Home / Misc.

Some games I remember playing or watching other people play were

• myst (soundtrack) (some scenes) this game was great. I never had the patience to solve it all myself without looking up guides online, but it was a ton of fun to explore the world and mythology regardless
• starcraft
• red alert
• neopets
• megaman

Wrap-up

Those are the main ones I remember playing! I also remember a pond ecosystem / toilet plumbing simulator (yes, one game!), but I think it is forever lost to time. Oh well, there’s more future to live!

What games do you remember playing in school?

Protip: If your game is on https://archive.org/details/software, you can often play it online right in your browser.

I needed to create some FASTA files of important regions of the human genome for work. BRCA1 & 2 are important in breast cancer research, SMA is implicated in  spinal muscular atrophy, and KIR and MHC are important for your immune system (e.g. why you have to have organ donor “compatibility”). I wrote a bash script that used Entrez Direct to automatically download these files from the NCBI servers.

FASTA files

If you just want the FASTA files to play with, they are here.

They were downloaded from the NCBI website and based on the NCBI Gene database coordinates against hg38.

source code

https://github.com/nouyang-curoverse/GA4GH_regions

This repository contains a link to download the final FASTA files, the ids.csv file I used as the master list of “mhc” and “kir” genes, the bash script file, and the xsl “xml transform” file I used to extract the information I needed from the xml file.

what i learned

Hey, what’s a gene anyway? If you use various databases (ensembl, ncbi, genenames, lumc, omim, lrg), you”ll get a whole range of coordinates for the same gene.

Take, for instance, BRCA2:

Start	End	Length	Source
32,889,611	32,974,403	84,792	ensembl
32,884,617	32,975,809	91,192	lrg
32,889,617	32,973,809	84,192	ncbi entrez
32,889,616	32,973,808	84,192	OMIM
32,890,598	32,972,907	82,309	COSMIC sanger
32,889,641	32,907,422	17,781	CGAP

 

In the end I standardized around using the NCBI Gene database and ignored the rest.

Hey, what’s the KIR gene region anyway? Turns out there’s a gazillion KIR genes, and there’s not exactly a “list” of them. Same for HLA. I just used my best human judgement and culled them from searches on NCBI Gene. From the git repo Readme:

For the HLA genes, I used the IMGT list of gene names, found at ftp://ftp.ebi.ac.uk/pub/databases/ipd/imgt/hla/fasta/ . For the KIR genes, I used NCBI Gene query to list all the KIR genes. http://www.ncbi.nlm.nih.gov/gene and "Homo sapiens"[porgn] AND KIR

The final list is in ids.csv.

The manual process was to download the FASTA file from the NCBI Gene database.

 

But for some genes, that is the KIR and HLA genes, each gene (e.g. just HLA-E) has many “alternate locii” versions.

Downloading these by hand would take days. Therefore, I needed to figure out a way to script this. My initial thought was to write a scraper using Google Sheet Scripts or a python library like Beautiful Soup. However, I thought this was dumb, because this NCBI Gene site is clearly the front-end to some database that hopefully had an API for programmatic access of some kind.

After a few days (seriously, this all took way longer than I thought it would) and with help from the biostars community I was able to figure out how to use Entrez Direct and write a bash script to automate the process for all the  genes.

(It has a hacky fix, where the bash script needs to be run again for each line in the file,

for run in {1..48} #change this!

 

I was too lazy to debug it that day and just wanted to get this finally done).

 

The source code is provided here, and contains reasonable comments and spits out some debugging info when you run it.

That’s all.

Leave a comment if you have questions 🙂

appendix

Emailed from me to ga4gh-dwg :

With help from biostars*, I finished pulling out the KIR and HLA regions and fixed the SMA region.

The updated collection may be publicly viewed at
https://workbench.qr1hi.arvadosapi.com/collections/download/qr1hi-4zz18-7zk4muy5grnaqpv/4qji0cfumh25dttlwteo6rj2b83z2b8vz1l0rja3uzo82bf3s/

The updated collection README and scripts are at
https://github.com/nouyang-curoverse/GA4GH_regions (the FASTA files are named by gene name and ncbi gene id, e.g. BRCA1-672.fa)

Of note, I did not mirror the IMGT HLA contents (ftp://ftp.ebi.ac.uk/pub/databases/ipd/imgt/hla/fasta/), even though that was requested on the minutes from the DWG meeting, due to their policy https://www.ebi.ac.uk/ipd/imgt/hla/licence.html .

Feedback appreciated!

Thanks,
–Nancy

*credit to https://www.biostars.org/p/122680/ and https://www.biostars.org/p/122522/