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June 28, 2011

Install DEIMS EML2Drupal Modules

One of the tools developed by the DEIMS group is EML2Drupal, a set of Drupal modules dedicated to generating EML compliant metadata for datasets using the DEIMS content types. This is a simple list of steps involved in setting it up - I'm pretty sure documentation exists on the project page but I like to have my own steps in instances such as these.

1) Visit the DEIMS Google Code site.
2) Download eml_config and views_bonus_eml
$ cd sites/all/modules
$ sudo wget http://deims.googlecode.com/files/eml_config.tar.gz
$ sudo wget http://deims.googlecode.com/files/views_bonus_eml.tar.gz

3) Unpack the modules
$ sudo tar -xzf views_bonus_eml.tar.gz

- Note: I applied a patch found here to allow anonymous users to access EML feeds.

4) Enable the modules (admin/build/modules)
- Bonus: Views Export EML
- EML Config

5) Configure EML Config
- EML Config store metadata that will appear in every EML document
- Complete the form found at http://yoursite.com/eml_config

6) Create a view for EML Feeds (eml_view)
- Key attributes: Type Node, Default + Feed displays
- Arguments: Node NID, Fields: Node NID
- Feed Display: EML Style,
- Provide as file: view-%view.xml, Inherits defaults
- Attach to: Default, Path: eml_view

7) Embed Default eml_view in the Panels Node Template for Datasets
- Node: Nid: Node ID
- Display Feed Icons

Next steps:

Unfortunately, Data Creator information is not part of the output EML file.

Posted by kkwaiser at 01:47 PM | Comments (0) | TrackBack

June 27, 2011

LAMP and Drupal on a Stick

File under: coolprojectsIneverthoughtI'dgetaroundto.

UMBS has a summer computer consultant and he has kindly agreed to help me figure out how to run Linux (and peripheral software) from a USB thumb drive. The Plan right now is to use Ubuntu 10.04 and expand that to include PHP, MySQL, Drupal and Data Turbine.

This page is for links but will hopefully contain notes as well.

Ubuntu forum with pointers

UNetbootin allows you to create bootable Live USB drives for Ubuntu,

Formatting options for USB - I.E., FAT, NTFS

On storage capacity of thumb drives - Looks like minimum is 4 gb, 8GB probably safe?

Apache on a stick (notice link within) - This is a Windows dependent install

Drupal on a stick wiki how-to - again using XAMPP!

Drupal on a stick page with links

Outdated instructions
with pointer to an installer (to good to be true?)

Posted by kkwaiser at 11:27 AM | Comments (0) | TrackBack

June 20, 2011


Water Sustainability and Climate (WSC)
Deadline: October 19, 2011
The goal of the Water Sustainability and Climate (WSC) solicitation is to understand and predict the interactions between the water system and climate change, land use (including agriculture, managed forest and rangeland systems), the built environment, and ecosystem function and services through place-based research and integrative models. Studies of the water system using models and/or observations at specific sites singly or in combination that allow for spatial and temporal extrapolation to other regions

Geography and Spatial Sciences (GSS)
Deadline: January 15, 2012, January 15, Annually Thereafter
The goals of the NSF Geography and Spatial Sciences (GSS) Program are:
- To promote the development and use of scientific methods and tools for geographic research

Advances in Biological Informatics (ABI)
Deadline: July 12, 2011 - Second Tuesday in July, Annually Thereafter
The ABI program accepts two major types of proposals: Innovation awards that seek to pioneer new approaches to the application of informatics to biological problems and Development awards that seek to provide robust cyberinfrastructure that will enable transformative biological research.

High-End Computing University Research Activity (HECURA)
Deadline: N/A
Accordingly, in 2009, the High-End Computing University Research Activity (HECURA) program invites research and education proposals in the areas of
metadata research;
access methods;
data management systems;

Instrument Development for Biological Research (IDBR)

Deadline: July 29, 2011, Last Friday in July, Annually Thereafter
supports the development of instrumentation that addresses demonstrated needs in biological research, in areas supported by NSF Biology programs (see http://www.nsf.gov/bio).

Long Term Research in Environmental Biology (LTREB)
Deadline: January 13, 2012 - January 13, Annually Thereafter
proposals that generate extended time series of biological and environmental data to address ecological and evolutionary processes and resolve important issues in organismal and environmental biology. Researchers must have collected at least six years of previous data to qualify for funding, and these data must motivate the proposed research.

Partnerships for Enhancing Expertise in Taxonomy (PEET)
Deadline: Current but no Longer Receiving Proposals
enhance taxonomic research and help prepare future generations of experts. Through this Special Biennial Competition in Systematic Biology, NSF will support competitively reviewed projects that target groups of poorly known organisms for modern monographic research.

Software Development for Cyberinfrastructure (SDCI)
Deadline: N/A
develop and deploy a set of reusable and expandable software components and systems that benefit a broad set of science and engineering applications.

Software Infrastructure for Sustained Innovation (SI2)
Deadline: July 18, 2011
intent is to foster a pervasive cyberinfrastructure to help researchers address problems of unprecedented scale, complexity, resolution, and accuracy by integrating computation, data, networking, observations and experiments in novel ways.

Strategic Technologies for CyberInfrastructure (STCI)
Deadline: Oct. 3-17, 2011; Feb. 1-15, 2012
to foster the development of a scalable, comprehensive, secure and sustainable cyberinfrastructure that supports potentially transformative research in science and engineering.

Sustainable Digital Data Preservation and Access Network Partners (DataNet)
Deadline: n/a
This solicitation addresses that challenge by creating a set of exemplar national and global data research infrastructure organizations (dubbed DataNet Partners) that provide unique opportunities to communities of researchers to advance science and/or engineering research and learning.

Posted by kkwaiser at 12:54 PM | Comments (0) | TrackBack

June 17, 2011

Convert TIFF file to IMG or other raster in ArcMap

After loading the TIFF files into an ArcMap window, simply right-click > Data > Data export.


Posted by kkwaiser at 03:39 PM | Comments (0) | TrackBack

Find files by extension in Linux/Ubuntu

Just taking note of a command I used today to locate a files of a particular type within a directory and child directories. For a better explanation, see the original source.

This command returns all hits which include .zip as part of the name and which are of type file:

% find . -type f -name "*.zip"

Posted by kkwaiser at 03:36 PM | Comments (0) | TrackBack

June 06, 2011

Summer Activities?

Time to think aloud. One of my goals for the summer is to engage students and researchers more. Get them thinking data and metadata early on. Here are a few ideas:

Data Management Presentation - Introduce basics of data mgmt. Potential targets = Courses with research project foci, Frontiers, REU, grad students
Data Entry overview - Introduce the Research Gateway to groups (Frontiers, REU) likely to contribute data.
GIS for mapmakers - Basic intro to ArcGIS with focus on local datasets and creating map layouts to describe research locale
GPS Scavenger Hunt - pre-allocate lats/longs for multiple groups and have them terminate at the same location. First group to the final location wins...something. Real prizes of somewhat-real value.

Mandatory IM Meeting - Discuss accomplishments, needed improvements, future goals, data collection, data policy

EML Module - deploy on Research Gateway

NSF DMP Language - draft for M. Hunter and others.

Posted by kkwaiser at 11:46 AM | Comments (0) | TrackBack