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December 23, 2009

Install Gallery2

One of the options for working with images in Drupal involves using the Gallery module which acts as a bridge to the Gallery2 opensource software package. Because the LTER content types used Gallery2, I'm installing it to evaluate whether or not to keep it in. Here's what I've done:

- Installed the Gallery module from Drupal
- Installed Gallery2 following this website.

$ sudo apt-get install gallery2
$ whereis gallery2
$ cd /var/drupal/
$ sudo ln -s /usr/share/gallery2/
$ dpkg -L gallery2

- Navigated to http://localhost/drupal/gallery2/install
- Following install wizard
- create login.txt and place in /usr/share/gallery2
- Standard installation...
- storage directory: /var/lib/gallery2/g2data
- set up a DB user through phpMyAdmin
- Set admin id
- installed all modules
- Errors:
* The ImageMagick module was installed, but needs configuration to be activated
* The Multiroot module was installed, but needs configuration to be activated
* The Nokia Image Upload module was installed, but needs configuration to be activated
* The URL Rewrite module was installed, but needs configuration to be activated

- Go to http://localhost/drupal/admin/settings/gallery and specify the URL as http://localhost/drupal/gallery2

- Skipped clean URLs of this step
- Did user synchronization

That's it for now. Merry Christmas.

Posted by kkwaiser at 04:32 PM | Comments (0)

December 22, 2009

Manage Images and Photos in Drupal

Photo and image management is not straightforward in Drupal. As an example, here is a list websites that appear helpful:

- A solid overview of many of the modules listed here.

- A tutorial on how to build an AJAX photo gallery using LightBox

- A list of websites that demo various Drupal photo/image modules.

- A tutorial on Image Picker.

- Possibly more related modules here.

And here is a list of modules that are potentially useful:

- Image
- Image Picker
- Lightbox 2
- Gallery integrates with Gallery2
- Image
- Inline
- Flickr
- Acidfree Albums
- Image Assist
- Embedded Media Field
- CCK Imagefield
- Imagefield Extended
- Imagefield Crop
- Image FUpload a bulk uploading module
- Image Cache
- Photos
Image Publishing

Posted by kkwaiser at 03:33 PM | Comments (0)

December 14, 2009

Pro's and con's of using a controlled (keyword) vocabulary

One of the many information resources that we need to standardize at the Biological Station is the list of index terms (i.e. keywords). In contemplating the creation of a controlled vocabulary for documenting data sets, bibliographic entries, study sites and research projects many decision points have arisen. Here is a summary.

Pro's of building a controlled vocabulary for indexing:

- Consistency within terminology can improve search ability. E.g., use of "forests" instead of "forest", "forests" instead of "trees", "carbon dioxide" instead of CO2

- Consistency across information resources. The same terminology will be used to describe data sets, bibliographic entries, study sites and research projects

- Incorporating external controlled vocabulary (LTER keywords) will facilitate integration of UMBS data resources with network-scale databases.

- Use of keyword auto-complete when creating metadata may yield use of more descriptive terms as compared to "top-of-the-head" categorization

- UMBS can make a contribution to the creation of a controlled vocabulary for use by other field stations and for ecology in general


- Building a controlled vocabulary can be time consuming

- Potential that keyword lists will not adequately represent new research directions

- No guarantee that anonymous users will use correct terms

Posted by kkwaiser at 01:00 PM | Comments (0)

Plan to create a UMBS controlled (keyword) vocabulary

Here is an outline of what will need to happen for the UMBS to have an established list of keywords.

1. Extract keywords from the UMBS bibliography, this will be the starting point.
- This list is not comma-delimited, meaning multi-term keywords will need to be manually identified and computer scripts will need to be used to reformat the terms and add commas

2. Parse the raw keyword list into 3 parts:
- a) keywords redundant with the LTER list (including synonyms and lexical variants)
- b) taxonomic descriptors (latin names and species-specific common names?)
- c) candidate-keywords for a UMBS keyword list.

3. Build UMBS keyword list using the candidate-keyword list:
- Identify how to treat hyphens, spaces and plurals
- Declare as equivalent lexical variants (e.g. analyze vs analyse)
- Identify synonyms
- Remove candidate-keywords that require context to make sense (e.g. "change", "description")


Savoy, J. (2005). Bibliographic database access using free-text and controlled vocabulary: An evaluation. Information Processing & Management, 41(4), 873-890.

Svenonius, E. (1986). Unanswered questions in the design of controlled vocabularies. Journal of the American Society for Information Science, 37(5), 331-430.

Svenonius, E. (2003). Design of controlled vocabularies Taylor & Francis.

Posted by kkwaiser at 10:59 AM | Comments (0)

December 11, 2009

Funding Opportunities for Field Stations

Took a look as some of the funding opportunities the Biological Station might qualify for. This is will be an ongoing list:

Funding Opportunity Comments
Improvements in Facilities, Communications, and Equipment at Biological Field Stations and Marine Laboratories (FSML) NSF, Harvard Forest just got one.
Improvements to Biological Research Collections (BRC) We can digitize and integrate our collections with others.
Major Research Instrumentation Program (MRI-R²)
Carbon and Water in the Earth System

Posted by kkwaiser at 04:10 PM | Comments (0)

Summary of initial keyword situation

An interesting question has arisen while formatting the Biological Station bibliography. What to do with all of those keywords? A quick and dirty analysis shows the keyword list from the bibliography has the following attributes:

3158 - number of keywords in the UMBS bibliography
2562 - number of keywords in the UMBS bibliography used 5 times or less
639 - number of keywords in the LTER Keyword list (v.0.9)
283 - number of overlapping keywords between UMBS and LTER lists

leaf graphic

(Right-click > view image for the fullsize image)

Here is a list of the 100 most used keywords in the UMBS Bibliography:

invertebrates 488
parasites 355
insects 317
aquatic 277
birds 272
distribution 270
water 267
species 260
behavior 252
plants 234
trematodes 231
description 229
forest 213
history 192
vascular 176
carbon 148
fungi 148
life 144
chemistry 141
snails 141
algae 132
succession 127
fishes 124
nutrients 122
vegetation 119
communities 118
breeding 114
growth 105
nesting 104
temperature 100
populus 99
change 97
nitrogen 94
bryophytes 92
dioxide 87
protozoans 86
mosses 85
reproductive 84
artificial 82
climate 81
success 80
development 76
diatoms 75
limnology 75
substrates 75
chemical 74
morphology 74
coleoptera 71
diptera 71
global 71
quality 71
soils 71
variation 70
aspen 69
biology 69
ecology 68
colonization 67
flora 67
vertebrates 67
benthic 66
predation 65
taxonomy 64
infection 63
population 63
biomass 62
production 62
trees 62
schistosomes 61
crustaceans 60
beetles 58
herbivory 58
size 58
larus 57
gulls 55
range 55
atmospheric 54
composition 54
deposition 54
feeding 54
periphyton 54
photosynthesis 51
acer 50
amphibians 50
lepidoptera 50
snakes 50
habitat 49
organic 49
wetlands 49
key 48
streams 48
leaf 47
structure 47
competition 46
light 46
mammals 46
molluscs 46
stagnicola 46
larvae 45
rana 45

Posted by kkwaiser at 12:52 PM | Comments (0)

December 08, 2009

Get Tabs working with CCK

When creating custom content types, you can group similar fields to make things a bit easier one the eyes. Going one step further you can break up the content type into separate tabs which will reduce scrolling time.

It's fairly easy to set up but there is a bug so I thought I should post this. Basically, the bug leaves the Help text out of the newly created tabs.

The modules I installed to get tabs working:
- Tabs 6.x-1.2 tabs-6.x-1.2.tar.gz (http://drupal.org/project/tabs)
- CCK Fieldgroup Tabs 6.x-1.0 (http://drupal.org/project/cck_fieldgroup_tabs)

To fix use the patch given here: http://drupal.org/node/559850

This is the file that is modified:

Posted by kkwaiser at 02:45 PM | Comments (0)

December 06, 2009

sftp in Ubuntu 9.10

For whatever reason, I have not been able to sftp to the LSA servers using FileZilla, the Nautilus browser (it crashes) or the terminal command:

$ sftp://servername.umich.edu

So I installed putty and putty-tools

$ sudo apt-get install putty

And have been able to get it working from the command line:

$ psftp servername.umich.edu

commands of note:
ls, cd, lcd, pwd, lpwd, put, get, mv
psftp> ls
psftp> put -r LTER_ContentTypes
psftp > ls /Dept/umbs/dept/


I've since gotten sftp via the terminal to work:

$ sftp usernamer@servername.umich.edu

to specify a port:
$ sftp -oPort=[portnumber] usernamer@servername.umich.edu

Posted by kkwaiser at 12:15 PM | Comments (0)

December 02, 2009

Work the Firewall in Ubuntu

Quick notes on how to firewall apache and open ports if needed:

This Ubuntu documentation is helpful.

This How To is the best.

$ sudo ufw enable
$ sudo ufw allow 22
$ sudo ufw deny 22
$ sudo ufw disable
$ sudo ufw status verbose

$ sudo /usr/sbin/apache2ctl restart
Allow an IP address through the firewall

$ sudo ufw allow from to any port

IP address shows up und inet addr:
$ ifconfig

File of concern:


Some delete statements:
$ sudo ufw delete deny from
$ sudo ufw delete allow from to any port 80
$ sudo ufw delete deny 80

Posted by kkwaiser at 11:01 AM | Comments (0)

December 01, 2009

Re-install Open Office on Ubuntu

For whatever reason, I could not open a dbf file with the Open Office Calc program. This is how I fixed it (not that I understand why this worked):

1. Started following this tutorial.

2. I was then getting a document recovery error so I install Java Runtime Environment following this tutorial. I also tried comment 1 out.

3. I still had a document recovery error so I tried this.

4. That still didn't do it so I tried this command:

$ sudo aptitude remove --purge openoffice.org

And for whatever reason, my new version of OpenOffice works and will open a dbf file. Unfortunately, that took up a lot of time.

Posted by kkwaiser at 04:53 PM | Comments (0)