BibTeX converter

Something worth trying out:

http://www.bibtex.org/Convert/

The longer I wait to write a paper in LaTeX, the more tools I will have at my disposal.

hah.

This would be the more flexible tool (which the above is based on): http://www.xandi.eu/bib2x/

color-code your 2D matrix

a.k.a. look at a 3D bar graph color-coded by height in plan view

Say you have a reasonably-sized matrix and you want to look for patterns in it. Let's define reasonably-sized as something on the order of 15 by 15, you care about what each value is, but it would be tedious to scan the matrix of numeric values.

Say your matrix is Z, maybe it is a 14x24 matrix of different exponents from polynomial fits to different variables using different thresholds or statistical parameters.

surface(Z) won't do exactly what you want because the values in the matrix will be the vertices of the surface, you want each grid box to be color-coded with the matrix values.

One way to do this is to make a 3D bar plot, color the bars by their height (matrix value), and then look at it in plan view. It's sort of cool.


figure;
h = bar3(Z);


% http://www.mathworks.com/help/techdoc/creating_plots/f10-19972.html
% Tell handle graphics to use interpolated rather than flat shading
shading interp
% For each barseries, map its CData to its ZData
for i = 1:length(h)
    zdata = get(h(i),'ZData');
    set(h(i),'CData',zdata)
    % Add back edge color removed by interpolating shading
    set(h,'EdgeColor','k') 
end
colormap('default')
colorbar;
grid off;
view([0,90])


% you can manipulate the axes (xmin xmax ymin ymax zmin zmax colorbarmin colorbarmax)
axis([0 25 0 15 0 1 0.8 1])


Here's the original document I got the code from:
http://www.mathworks.com/help/techdoc/creating_plots/f10-19972.html

Here's an example of the output.
The rows, 1-14 are 14 different polynomial fits.
The columns, 1-24 are 24 different ways of calculating the x variable in the fit (different thresholds or filters).
The value is the Rsquare value, colorbar color codes it from 0.8 to 1.0.

The matrix shows that the 1st and 23rd-25th columns have the worst fits for all 14 relationships. Also, rows 4, 5, 11, 12, 14 do not produce well-behaved polynomial fits.

Really I just think it's a nice quilt pattern.

As an added plus you can use the rotate button to look at it from any angle you want.

encouragement

Encouragement to an early-career scientist (me) in an email:  (I had replied to his earlier email which questioned our recent publication and asked if he would like to contribute any datasets to a relevant database for bedload transport.)

Although I coauthored publications concerning datasets and data needs with respect to sediment and bedload and founded a relevant organization (attached), this topic is at the very best very complex and I advise to reconsider spending any of your time on a process which you have studied, upon your admittance, little.


Always great to have encouragement from the wise elders of the field.

It's sort of like when Ice-T (wise elder) told Soulja Boy (early career rapper) to "Eat a Dick" for "single-handedly killing hip hop." In his youtube reply, Soulja Boy was none too pleased, but I remember him saying something useful like "Why don't you give me some constructive advice instead of telling me to eat a dick." (paraphrasing)

Oh well, I just drew an analogy between myself and Soulja Boy. At least I have that.

example database

Here is an example of a database that is supposedly popular in its discipline. Wonder how.

Paleobiology Database

http://paleodb.org/cgi-bin/bridge.pl

hubzero

http://hubzero.org/

HUBzero® is a platform used to create dynamic web sites for scientific research and educational activities. With HUBzero, you can easily publish your research software and related educational materials on the web.

That is all I know for now but I hope to learn more.

geodata workshop report

Outcome of the GeoData meeting:

http://tw.rpi.edu/media/latest/WorkshopReport_GeoData2011.pdf

"A scientific culture change in regard to modern data is underway but must be accelerated."

That would be nice.

Part of the tetherless world constellation:

http://tw.rpi.edu/web/

The meaning of TWC seems esoteric to me.

startup.m (2)

A long time ago I wrote about setting defaults in startup.m.

Today I finally got to running my new MATLAB on my new computer and have been doing things like setting the path and specifying startup.m.

It is probably safer not to rely too much on startup.m, because if you write a program and then send it to someone else, who hasn't set default font and linewidth and etc. like your own startup.m, then things can get ugly.

I set two things in my startup.m (which is placed into a folder near the top of my path)

(1) MATLAB will open up to a specific folder:
cd C:\Users\me\Documents\MATLAB

(2) log everything I type into the commandline into a date-specific text file

diaryname = ['diary\' datestr(now, 'yyyy-mm-dd') '-diary.txt'];
diary(diaryname);


I'm pretty pleased about these two things. 

earthcube (2)

You can join the EarthCube community here:

http://earthcube.ning.com/

Typical statement:
The goal of EarthCube is to transform the conduct of research in geosciences by supporting the development of community-guided cyberinfrastructure to integrate data and information for knowledge management across the Geosciences.


There is also a link for a questionnaire about science/data requirements gathering. I don't know exactly what that means but I'm going to find out.

https://www.surveymonkey.com/s/GeoSciRequirements

data publishing ditty

A short article about data publishing and technology.

http://blogs.wiley.com/publishingnews/2011/06/28/it%E2%80%99s-what-counts-how-data-transforms-our-world/

Mentions DataCite, Mendeley, and Scribd.

Data management plans are becoming increasingly integral to project funding proposals – and will continue to become more stringent. However, both services (e.g., global standards, long-term curation) and incentives (such as academic credit, enforceable policies, and funder metrics) need to be overhauled in order to provide people with the resources and operability they need.


The current mismatch was illustrated by Todd Vision (DRYAD). Quoting a recent PARSE survey, he noted that there is a major discrepancy between researchers’ apparent willingness to share data (85%) and current levels of actual compliance with requests or funding mandates (27%).

metadata conference

There is an entire conference about metadata and vocabularies. This is insane. But important. I actually wish I could learn all the content about the conference without actually traveling.

Program:
http://dcevents.dublincore.org/index.php/IntConf/index/pages/view/program-2011

Metadata people say "Dublin Core" a lot and until you know what that is, it is very perplexing.

Dublin Core (from wikipedia):

The Dublin Core set of metadata elements provides a small and fundamental group of text elements through which most resources can be described and catalogued. Using only 15 base text fields, a Dublin Core metadata record can describe physical resources such as books, digital materials such as video, sound, image, or text files, and composite media like web pages. Metadata records based on Dublin Core are intended to be used for cross-domain information resource description and have become standard in the fields of library science and computer science. Implementations of Dublin Core typically make use of XML and are Resource Description Framework based.

mamp

mamp stands for Mac, Apache, MySQL, PHP.

http://www.mamp.info/en/index.html

"manage your websites locally"

we shall see.

README says:

README for MAMP 2.0

- Put your HTML and PHP files in the htdocs folder!
- Database files are stored in the folder db/mysql or db/sqlite.
- PHP errors are logged in the file logs/php_error.log. If you doubleclick the logfile, the console will be open, which show the last errors.

How to create a local environment using MAMP
http://drupal.org/node/66187

vim

I just installed macvim as a new text editor.

I still remember a command or two for vi.

Ready for my life to be changed now.

http://code.google.com/p/macvim/

I plan to do a lot of search and replace by script.
Maybe some html editing instead of in seamonkey.

earth cube

I'm adding a new topic to this blog, cyberinfrastructure (to take NSF's out-of-date word). And I'm not going to add propriety either. I considered having a new blog about geoinformatics but now I've decided that I should just add to the list of topics in matlabor. (Currently something like (1) matlab (2) GIS (3) stuff I like.)

In these new posts I will attempt to capture the interesting events and topics in the deluge of emails and announcements I get.

Random: I was thinking of building a matlab program to analyze Eminem lyrics.

Anyway, the first cyberinfrastructurey post is about Earth Cube.

http://www.nsf.gov/geo/earthcube/index.jsp

NSF ... recognize(s) the multifaceted challenges of modern, data-intensive science and education and envision an environment where low adoption thresholds and new capabilities act together to greatly increase the productivity and capability of researchers and educators working at the frontiers of Earth system science.

Writing about cyberinfrastructure often has a lot of very long sentences.

GraphClick - digitize points

mp told me about this one: GraphClick

http://www.arizona-software.ch/graphclick/

She is using it to digitize grain size distributions. I used it to digitize contours of the damage zone around Wenchuan earthquakes from historical documents and volume of continental crust through earth time curves. You need to pay the $8 to get all the features (like saving more than 10 points), but it is well worth it, and you can try it out before paying.

I LOVE useful software.

It is for mac only I think. sigh.

parsing text with Text to Columns

This is one of those things that you just want to hit yourself on the head for not knowing earlier.

In Excel (yes, I still use excel) there is a Text to Columns Wizard that allows you to parse data by either fixed width or a defined delimiter.

In Excel 2011 Mac (gag), it is under Data --> Text to Columns.

PARSING BY FIXED WIDTH IN EXCEL!

This is especially useful for delimiting degrees, minutes, seconds. Use it with Search and Replace to do what you need to do.

It is really sad that I just learned this today.

setting up figure templates

Make your life easier by setting up figure templates for MATLAB

http://gears-tt.blogspot.com/2011/03/templates-why-matlab-is-awesomeness.html

As posted by MATLAB stream on fb.