learned and not forgotten

bash shell scripting

# basic for loop
for i in `ls *`; do echo $i ; done

scared skinny?

overweight moms are/have:

4 x more likely to get gestational diabetes
2 x as likely to have high blood pressure (increased blood clots, stoke, death)
higher chance of C-section (18% instead of 11%)
babies 2 x more likely to have spina bifida, 0.3 x as much heart defects

2/3 maternal deaths in US are related to complications from obesity.

http://healthland.time.com/2012/03/12/how-moms-weight-before-pregnancy-can-affect-a-babys-brain/

While it’s not entirely clear how a woman’s weight before conception may impact her baby’s brain, Helderman says the leading theory involves inflammation. Excess weight can keep levels of potentially destructive immune cells high; these are the cells that rush to the site of trauma to clear away debris. Studies show that inflammation can adversely affect the brain, and it’s possible that an expectant mom’s heightened inflammatory response could filter through to her developing baby.

Read more: http://healthland.time.com/2012/03/12/how-moms-weight-before-pregnancy-can-affect-a-babys-brain/#ixzz2RyxIBgzs

caffeine content

Caffeine in Chocolate
Ghirardelli 72% Cacao Twilight Delight: 22mg per 17g square
Ghirardelli 86% Cacao Midnight Reverie: 20mg per 13g square
dark chocolate in general is 28 mg per 1.4oz (40g)
1 oz (28 g) Cadbury (small) bar is 15mg
milk chocolate in general 3-10 mg per 1.4 oz (40g)

Caffeine in Tea
Black Tea: 23 - 110 mg Oolong Tea: 12 - 55 mg Green Tea: 8 - 36 mg White Tea: 6 – 25 mg

Drink green, white and lightly oxidized oolong teas are good choices, as they tend to benefit from lower water temperatures and shorter steeping times.

Guidelines
Adverse effects have been reported when pregnant women consume more than 200mg a day.

I aim to have less than 100mg a day, which would be:
- 1 green tea and two Ghiradelli squares
- three Ghiradelli squares

pre-pregnancy list

- preconception checkup
- ask about immunizations, get a flu shot
- take 400 mg of folic acid a day for one month before conception and during first trimester
- make sure that your multivitamin doesn't contain more than 770 mcg RAE (2565 IU) of vitamin A, unless it is in beta-carotene form
- don't drink during last two weeks of cycle (or at all)
- limit caffeine to 200 mg per day
- get my BMI below 24 (160lbs would be 24.3, 158lbs would be 24.0)
- don't eat: shark, swordfish, king mackerel or tilefish
- don't eat more than 6 oz per week of: chunk light (solid white and albacore are worse) it's good when it comes from skipjack and bad when it comes from yellowfin
- do eat two servings of fish a week: salmon, herring(Atlantic, jack, chub), farm-raised rainbo trout, sardines, whitefish
- floss
- call insurance about prenatal coverage, ask about deductibles, tests and procedure covered
- avoid soft cheese, cold deli meat, raw fish, unpasturized juice

Grep Regex

grep "twitter \|wikipedia " filename # grep for A or B
grep -P "twitter |wikipedia " filename # grep for A or B
grep "\\\\" filename # grep for a single \

grep -P "\t" filename # grep for tab

grep -h - suppress filename content is found in
grep -A 2 - returns matching line and to lines After
grep -B 2 - returns matching line and to lines Before

Grep Regular Expressions

grep regex
http://www.bo.infn.it/alice/alice-doc/mll-doc/usrgde/node28.html

more about unicode hex etc

common python snippets

Python Modules http://wiki.python.org/moin/UsefulModules

regex subsitution in myString

myString= re.sub("$[0-9][0-9]*$", "", myString)
myString= re.sub("\\\\", "", myString) # remove a single backslash
myString= re.sub(r"\\", "", myString) # remove a single backslash using a "raw string"

string substitution (*not* for regex)

c = c.replace(u'\xae', '') # ®

c = c.replace(u'\xbb', '') # »

c = c.replace(u'\x99', '') # char for TM

c = c.replace(u'\xa9', '') # ©

c = c.replace(u'—', '-') # replace mdash u2014 with regular dash

c = c.replace('?', '') # ?

c = c.replace(':', '') # :

c = c.replace(';', '') # ;

save regex-matching string to a new variable
pageObj = re.search("od [0-9][0-9]*", pagetext)
if pageObj:
pageObj2 = re.search("[0-9][0-9]*", pageObj.group())
numb = pageObj2.group()
print "numb is ",numb
pages = range(2,int(numb)+1)

for p in pages:
newUrl = locUrl+'afpg/'+str(p)+'/Default.aspx'
print "adding ", newUrl

stuff to write about

BIO notation

Inside-Outside Algorithm

HPSG

HPSG (Head-Driven Phrase Structure Grammar)

Stanford and Berkeley espouse this syntactic theory.
It is a "highly lexicalized, non-derivational generative grammar theory."
It is a type of phrase structure grammar, as oppsed to a dependency grammar (The syntactic trees I learned are dependency grammars).

sed one-liners

sed 's/ Телефон: /\t/' filename # basic search and replace

sed 's/ [-] .*//' filename # put tricky chars in []

sed 's/\&amp/\&/' filename # example of escaped char

sed 's/.\{1\}/& /g' filename # insert 1 space between each char

sed 's/.\{2\}/& /g' filename # insert 2 spaces between each char

sed 's/$.*$\/word$/word\1/' filename # search and replace with a captured pattern () on LHS and \1 on RHS

sed 's/word/&\n/' filename # search and replace insert a newline
sed '/^\s*$/d' filename # delete blank line

Good resources for one-liners with examples http://sed.sourceforge.net/sed1line.txt

Starting Off in Python

We’ll start off by looking at material from these sites.
http://www.astro.ufl.edu/~warner/prog/python.html
http://www.sthurlow.com/python/

http://learnpythonthehardway.org/book/ <- recommended for new programmers

free online courses

http://www.udacity.com/ <- cs classes
http://coursera.org/

http://www.khanacademy.org/
http://www.khanacademy.org/#biology
http://www.khanacademy.org/#computer-science
UnCollege.org has a nice collection of online resources, including a lot of computer science resources: http://www.uncollege.org/resources.

- MIT Open Course Ware: http://ocw.mit.edu/courses/#electrical-engineering-and-computer-science
- Google Code University: http://code.google.com/edu/
- Stanford's Education Everywhere: http://see.stanford.edu/see/courses.aspx

using "screen" command to handle multiple sessions

from http://www.cyberciti.biz/tips/linux-screen-command-howto.html

$ screen -S 1
CTRL+a, c -- create another screen window
CTRL+a, n -- switch to next screen window I've got open

To list all windows use the command CTRL+a followed by " key (first hit CTRL+a, releases both keys and press " ).
To switch to window by number use the command CTRL+a followed by ' (first hit CTRL+a, releases both keys and press ' it will prompt for window number).

Common screen commands

screen command	Task
Ctrl+a c	Create new window
Ctrl+a k	Kill the current window / session
Ctrl+a w	List all windows
Ctrl+a 0-9	Go to a window numbered 0 9, use Ctrl+a w to see number
Ctrl+a Ctrl+a	Toggle / switch between the current and previous window
Ctrl+a S	Split terminal horizontally into regions and press Ctrl+a c to create new window there
Ctrl+a :resize	Resize region
Ctrl+a :fit	Fit screen size to new terminal size. You can also hit Ctrl+a F for the the same task
Ctrl+a :remove	Remove / delete region. You can also hit Ctrl+a X for the same taks
Ctrl+a tab	Move to next region
Ctrl+a D (Shift-d)	Power detach and logout
Ctrl+a d	Detach but keep shell window open
Ctrl-a Ctrl-\	Quit screen
Ctrl-a ?	Display help screen i.e. display a list of commands

awk

specify tab-delimited columns
awk -F'\t' '{ print $1}' file

print column $13 and column $10 where $13 matches "MY"
awk -F"\t" '$13 ~ /MY/ {print $13"\t"$10}' | less

awk -F"\t" '$7 == "restaurant" ' japan.osm.poi > restaurants

awk '{ print \$1} ' file, print 1st column, escape $ when in perl system command

not really sure what this does.....

awk -F "\"*,\"*" '{print $3"\t"$5}' jigyosyo.csv

iconv and recode to change file encoding

List all the encoding codes:

iconv --list

iconv --from-code LATIN1 --to-code UTF-8 --output adoos.com.my.categories.zlm-MYS.UTF.txt adoos.com.my.categories.zlm-MYS.LATIN1.txt

recode ....

learned and not forgotten

bash shell scripting

scared skinny?

caffeine content

pre-pregnancy list

Ling Links

health: probiotics and mood

family tree software