A Fluid Grid

It's true

2011-05-02T16:17:00.001-04:00

One of my favorite bloggers said this, which is true even of my mother (who swears she is a democrat, but watches Fox news religously and hasn't voted democrat in I don't know how long). I think these words essentially sum up what most of America thinks right now, "Everybody likes the idea of smaller government until they see it." Bingo.

"I keep telling my conservative in-laws that they really don’t want smaller government. They just want to pay less taxes, which I can understand. Everybody likes the idea of smaller government until they see it."

Free citation managers

2011-03-30T15:32:00.000-04:00

I needed to make a quick, properly-formatted bibliography and I'm not lucky enough to get one of our corporate Endnote seats. So I turned to Zotero, a project that I've been following but not really using (same with cb2bib). I entered the refs, used the Word 2007 add-in, cited, created the biblio, and feeling proud I called a colleague to ~~show off~~ share this handy tool. Her response was, "Oh, I don't need that, I use Mendeley." Men-what? And so I embark on a new round of research in an attempt to stay up-to-date with a software and data landscape that changes daily.

Looks like both products offer (or are about to offer) a stand-alone desktop tool (e.g, no need for a browser). Mandeley appears to be free, but not Free (proprietary and developed by a company). Zotero appears to be primarily developed by George Mason University. Both offer extensive import/export from the relevant data data types (Bibtex, etc.) but we do some funny things with attributes so I'll have to check our mileage. There seems to be some religious battles regarding usability - and I've struggled with a few citation managers here, so this makes sense. Other than that I need a beer, pizza, and some time without work or kids to compare these two. Until below are some other quick notes. More to follow...

Mendeley
Mendeley is a free reference manager and academic social network that can help you organize your research, collaborate with others online, and discover the latest research.

Features from their website:

General

Cross-platform - Mendeley Desktop has full support for Windows, Mac, and Linux.
Secure backup - Any documents synced in the desktop client will be backed up on the web.
Mobile devices - Read papers anywhere with your iPhone, iPad, or iPod Touch.
Install on multiple computers - Install Mendeley on multiple computers and access your entire library.

Organize

Full text search - Mendeley Desktop creates a fully searchable database of your papers.
Automatic metadata extraction - We automatically extract metadata from the papers you import.
Highlight and annotate - Organise your own notes and highlights and share them with others.
Flexible organization - Groups, tags, and filters let you organise your way.

Community

    Research collaboration - Use research groups to collaborate with your peers and colleagues.
    Trends and statistics - Get real-time readership statistics and view trends in your research area.
    Track your own publications - Find out how many people are reading and downloading your own research.
    Related research - Get personalized suggestions on interesting papers to read.

Integration

Microsoft Word / Open Office - Our plugins let you easily insert bibliographies into your documents.
BibTeX / Endnote / RIS - Mendeley Desktop can import and export all these formats and more.
Zotero / CiteULike - Mendeley Desktop can sync with your Zotero or CiteULike libraries.
Mendeley API - Our API allows 3rd parties to build applications using Mendeley's data.

Zotero
Zotero [zoh-TAIR-oh] is a free, easy-to-use tool to help you collect, organize, cite, and share your research sources. It lives right where you do your work—in the web browser itself.

Features from their website:

Collect Everything - Record your online research with one click.

Capture Research Data - Collect information on books, journal articles, and other resources with a single click in your location bar
Archive the Web - Archive entire web pages in your library
Store Anything - Store related PDFs, files, images, and links in your library

Organize Any Way - It has never been easier to organize research.

Intuitive Interface - Zotero's iTunes-like interface allows you to quickly organize your research sources
Drag and Drop - Drag and drop items into collections and tag them with terms relevant to your needs
Take Notes - Easily take notes right alongside your items

Cite Anywhere - You're never more than one click from a bibliography.

Drag and Drop Bibliography - Drag and drop bibliographies anywhere: into an email, a blog post, or any word processor
Word and OpenOffice Integration - Plugins for Word and OpenOffice make it easy to drop in references on the fly
Cite in Style - Zotero comes preloaded with all major styles, and thousands of additional journal-specific styles are freely available

Access Everywhere - Your information is wherever you need it to be.

Work Locally, Sync Globally - Get the best of both worlds: Work locally with your research materials and automatically sync your data between multiple computers
Browse from Mobile Devices - Even without Zotero, you can access your collection from any web browser. You can even view your collection on mobile devices like the iPhone.
Publish Your Process - Share your research with the world and make your library and collections public

Collaborate with Anyone - Opt in to automatic collaboration.

Share Group Libraries - Create group libraries to collaborate with other Zotero users
Publish Dynamic Bibliographies - Publish shared libraries for your organization, class, or research group
Uncover New Connections - Discover other researchers working in your field

Relevant Links
http://chronicle.com/blogs/profhacker/using-mendeley-for-research-management/25627
http://forums.zotero.org/discussion/6174/mendeley/
http://spinuzzi.blogspot.com/2010/03/sxswi-discussion-mendeley.html
http://astuscience.wordpress.com/2010/05/20/the-most-successful-post-paper-versus-mendeley-zotero-and-stuff/
http://earlycj5.wordpress.com/2009/03/20/zotero-vs-mendeley-initial-thoughts/
http://en.wikipedia.org/wiki/Comparison_of_reference_management_software
http://groups.google.com/group/zotero-evangelists/browse_thread/thread/2fc26735b1142acd?pli=1
http://www.slideshare.net/giustinid/ref-works-mendeley-zotero

Some notes about MySQL configuration

2011-03-24T12:22:00.000-04:00

MySQL is so easy to just "get running" and my applications are often quite basic. So, I only get around to actually "configuring" MySQL every couple of years, during which time I've forgotten the guidelines. So this is this year's refresher reading list:

http://www.mysqlperformanceblog.com/2006/05/17/mysql-server-memory-usage/
http://dev.mysql.com/doc/refman/5.0/en/innodb-configuration.html
http://www.mysqlperformanceblog.com/2011/03/21/what-causes-downtime-in-mysql/
http://www.mysqlperformanceblog.com/2011/02/17/how-to-syntax-check-your-my-cnf-file/
http://fts.ifac.cnr.it/cgi-bin/dwww/usr/share/doc/mysql-server-5.0/examples/my-large.cnf.gz
http://mysqldatabaseadministration.blogspot.com/2005/11/mysql-5-optimization-and-tuning-guide.html
http://brian.moonspot.net/2008/05/06/example-mycnf-files/
http://forge.mysql.com/tools/tool.php?id=138
http://forge.mysql.com/tools/tool.php?id=137
http://www.pythian.com/news/1067/difference-between-innodb_data_file_path-and-innodb_file_per_table/
http://forum.percona.com/index.php/t/1493/

More to follow...

Some notes about MySQL configuration

2011-03-24T09:30:00.001-04:00

Even More Mercurial: sub-repos

2011-02-22T21:01:00.001-05:00

http://lazymalloc.blogspot.com/2008/05/managing-multiple-repositories-with.html
http://kiln.stackexchange.com/questions/874/cannot-figure-out-subrepos/1768#1768
http://semver.org/
http://hg.python-works.com/ - this is actually pretty cool. Looks like we need a repo per project. This should speed up repo and user management.

Even More Mercurial: sub-repos

2011-02-22T20:45:00.001-05:00

http://kiln.stackexchange.com/questions/874/cannot-figure-out-subrepos/1768#1768
http://semver.org/
http://hg.python-works.com/ - this is actually pretty cool. Looks like we need a repo per project. This should speed up repo and user management.

Even More Mercurial: sub-repos

2011-02-22T20:24:00.001-05:00

http://kiln.stackexchange.com/questions/874/cannot-figure-out-subrepos/1768#1768

A version of change

2011-02-21T09:41:00.001-05:00

You know how you know you need to do something... you want to do that thing... you NEED to do that thing eventually... but the law or inertia just works against you? I know you've been there. Well, our IT development shop has been there for years. We've been rocking CVS as our version control system (VCS) for years (on the same server), and it's actually been OK. But some of us have seen the day of change coming for a long time now... or at least I have. The CVS is now past its prime and with new hardware we are poised to replace software as well.

Our shop often works on small projects and our developers have to work with just about every development technology known to man -- often in the same day. We grew up doing Java/Oracle mostly, but find ourselves living in .Net world these days. So Visual Studio integration would be a nice change for folks. Our guys and gals just want to focus on programming and do not want to deal with learning something ELSE new so a lower learning curve will initially seem more beneficial. In this vane, we currently don't use a distributed VCS model nor we do likely need one (but, maybe there's some benefit here we're not thinking of).

Our projects range from small to medium-large in terms of code, though we often abuse CVS by sticking non-code in it. So, speed is not a HUGE issue, but I'm sure everyone would appreciate a speed up. Everyone knows we need to improve our tagging/branching/merging, so a VCS that helps us do this easily/safely and doesn't get in our way is desirable. Our company is pretty much Microsoft across the infrastructure board, but we rock the occasional Linux server. Our local backup is being augmented by the enterprise over-the-wire Microsoft solution that sends daily changes back to the HQ. So, we'll likely shift to a VCS that happily (natively?) runs on Windows.

So, tonight I've done more reading (been thinking about this for years) and determining the next CVS lilly pad is going to me more challenging than ever. It seems that all of the leading contenders have matured greatly.

Candidate 1 - SVN

Subversion seems to be adequate. We don't need distributed VCS and there are a lot of tools out there for it. Some of the disk and speed issues seem to have improved over the years, but likely are still issues. SVN likely offers the lowest learning curve for folks, but we also don't gain as much from it. Oh, and the migration from CVS seems to be mature. There do seem to be Windows native installations possible.

Candidate 2 - Hg
Distributed VCS, decent documentation and rich tool sets. Learning curve will be steeper than SVN. Performance should be better than SVN, but not as fast as Git. Its python based and seems to be Windows native. I need to read more about CVS migration and how simple you can make using it (can you do central version management if you want to?). A little more reading from somewhat older links indicates that we will have a hard time following a centralized model with mercurial (though that may be a good thing).

The Rest - Git and Bzr
Git and Bazaar are both annoyingly compelling and mature. I'm going to ignore them for now however as I can't see anything that they do differently than what Hg does -reletive to our need.

Bzr seems like it is very flexible, but the toolset seems a little behind Git and Hg. Plus, it still seems to support Linux better than Windows given the competition developers seem to focus more on Hg and oddly Git for tool/integration outside of Linux.

Git is powerful and has some huge momentum. But the learning curve sounds like it's steepest here. That said, the existing toolset and mindshare to support them, particularly on Windows, seems to be present and not losing steam.

So, we don't have a decision yet, but I've provided some links below for more information.

Bazaar (bzr)

Subversion (svn)

Mercurial (hg)

Git (Git)

Comparisons

Instructions, Tutorials, Stories

I've been waiting for..

2011-02-20T10:48:00.003-05:00

James Fee called out two topics that I've been waiting for but failed to monitor. One is the maturation of an OpenLayers-eqsue, Flash-based mapping framework called OpenScales. We like building stuff in Flash and I remember being excited when I saw that OpenScales had started on the OpenLayers mailing list. I'm glad to see it achieve such maturity as an alternative to the ubiquitous OpenLayers (which also rocks).

The other topic relates to a running thought that I've had, "This SLD stuff ~~sucks~~ is too complex and time-consuming to produce for 90% of my needs. I wish there was a KML for styling - something that covers most of what I need but is simple to hack on." At the back of my mind I guess I was thinking about CSS for maps, or a something like a Mapserver Mapfile but for broader use. Behold Carto. It's quite limited now as far as as the platforms its used in. But I hope similarly easy approaches (below) emerge as a wider alternative to SLD.

From the carto page, "We've been actively using and contributing to the Cascadenik project for several years, so it doesn't come as a surprise that Carto is heavily inspired by Mike's pioneering work in Cascadenik. We hope that our work on Carto will contribute to the emerging field of CSS-like map styling which includes projects like GSS and MapCSS and the GeoServers CSS Module"

Post-pre - Pre

2009-06-23T09:16:00.000-04:00

I do not like wikis, SharePoint and a good many products from Microsoft. This includes Windows on phones - even the sexy new OS (tried it on the HTC Touch Pro and took it back immediately). My nerd-friends know this. These friends also know that we are a Sprint family for better or worse (we've had respectable service from the Sprint network and honestly we've always found them to provide excellent customer service and value as well. They also are willing to admit when they screw up and will cut you a deal. Verizon and AT&T do not want your business badly enough to incentivize you to stay). So, as a Sprint user, iPhone is out for now. Verizon's phones have never spoken to me, though Blackberry's would work fine if I could use them with my work email servers and not pay extra.

So, what I know is that I'm staying with Sprint for a while. This really should be OK because all I need is a phone with a modern browser, an OS that doesn't get in my way ( Windows), syncs with M$ Exchange, top-notch calendaring/contacts/texting, and is responsive. I also must have a vertical keyboard and will pay extra for a physical keyboard. So, I'm left with Crackberry and some device from our friends at Palm. As a historical Palm user (currently running a Centro after many years with a Treo 650), I will stay with Palm. Therefore, after all this I will eventually own a Pre.

I've been watching the reports about the Pre and all the comparisons to the iPhone. Firstly, if I wanted an iPhone badly enough I would switch to AT&T -- I don't have to have an iPhone. I just need a phone that provides many of the same benefits as an iPhone - and in my case I also want a physical keyboard. I do not consider the Pre as an iPhone-wanna-be, I see it as just another "modern" phone (with "modern" once again defined for us by Apple).

The reports I've also seen speak about the let-down some people have had with the Pre (poor quality, still missing SDK, anemic selection of apps). I'd be lying if I said these reports didn't sadden me a little. But, I'm willing to cut Palm some slack as they rapidly push out a huge new platform - there will be bugs/issues. That said, I really need Palm to get the Pre platform cleaned up and silky smooth within 6 months. It seems like they have a trajectory to do that. But they still have some major hurdles.

Spatial DBs and Jumping Java

2009-04-09T10:53:00.000-04:00

Some news clips from projects that I find fascinating: The anticipated 2.3.0 cleanup release of SpatialLite is now out. Building on the highly efficient, blazing fast, feature-rich and highly-embeddable SQLLite , this geodb data store and engine might be a good option to address the call in the Shapefile 2.0 manifesto. I agree with the thoughts in the manifesto (I'm sick of managing many little files) and I'm all about keeping things simple, focused and efficient. So I'm going to watch this project with interest especially since spatial support in MySQL is going no where fast.

Also, after a long wait, Open JUMP is out with a new version. We dabbled with this years ago but got sick of Java-based desktop apps. In fact, recently we are finally getting on the .Net bandwagon and are working with MapWindows. Though I guess we are using Java a little on the desktop through our CUPSS [1][2] [3] project (it uses Trolltech/Nokia Jambi that wraps Qt with Java). We generally have had to get away from supporting systems other than Windows for a variety of reasons :-( Hopefully we'll be able to get back into the platform-agnostic game soon.

ESRI Dev Summit Keynote: SOAP vs REST

2009-04-07T15:11:00.000-04:00

Watch this if you are involved in web services . Period.

http://www.spatiallyadjusted.com/2009/04/07/esri-posts-david-chappells-2009-developer-summit-keynote/

Also, if you want to see the power and sexy appeal of the ESRI Flex API, behold this
http://www.mdimap.com/imap/

Move to the cloud

2009-04-01T11:20:00.000-04:00

For a group like mine that writes software for modeling and other computationally intensive code from scratch, moving code from early 2000-era single CPU approaches to SMP approaches (or even clustering) is a painful but probably required undertaking. We've discussed it, but the business cases (or the requests in the way of $$) have not materialized so we didn't fix what wasn't broken.

But, I wonder if we should just skip all of this and move the model to take advantage of the flexibility of cloud computing. Enterprise providers are convinced Cloud will scratch many itches and announcements like this ( [1] [2] [3]) Sun and IBM's investment in Cloud, and Cisco's leap of faith into building server fabrics because, "[cloud computing] is the future of the data center. It will evolve into clouds and change business models forever" make the question compelling.

For us in the niche world, we have to ask does the investment make sense? Where does Cloud stop being useful? When is it best used? When should you not use it?

When your background data don't change

2009-03-31T12:54:00.000-04:00

I am watching the MapTiler project closely now. I once started to look into the GDAL2Tiles utility to scratch an itch I had for making simple online maps from data data would not change with any real frequency (never -> semi-annually). The itch went away so I stopped playing around, but it was a reasonable option at the time.

Now that the project has a GUI and someone providing care and feeding, I also have had the itch return. So, I might get a chance to run with this ball after all.

I am really enjoying watching the OSgeo ecosphere mature as the standards of WMS, TMS, GeoJSON, GeoRSS, KML, etc seep into the industry. It is just getting ridiculously easy to integrate stuff in basic ways.

Notes from Fee

2009-03-31T12:37:00.000-04:00

James Fee has some good notes from the ESRI Dev Summit this year. He also has a nice show regarding using the Openlayers API against services from ArcGIS Server. The exact support for ESRI-specific services in OL 2.8 depends on what came out of the 2.8 release triage meeting.

I am excited about the prospects of true OL support for ESRI services.

If you follow this thread through to the end, it sounds like there is some chance that Arc* support will make it into the 2.8 OpenLayers release at least in experimental form.

I feel compelled to reuse the Lord of the Rings quote in a techy context (I know this is getting cliche):

"One framework to rule them all, one framework to find them, one framework to bring them all, and in the darkness bind them."

Eat your planet

2007-12-09T10:14:00.001-05:00

I wake most mornings and feel like Marvin the Martian after he blaster the planet out from underneath him. In my case I'm eating the planet out from under me. As a human, and in particular an American, I have the compulsion to always "want more" and the brains and adaptability to always get it. As an American I am programmed to consume and my society "gives" me the fuel and the means to keep consuming more from this dumb, unsustainable Open Loop System. I've seen this for as long as I can remember, and I bet you have too. But man, it's tough to re-program yourself. I applaud those who have.

Here some very smart people have explained the Story of Stuff, and how we can close the loop.

EPA's Experiment in Community Building

2007-12-01T08:57:00.002-05:00

I thought you might be interested in how the US federal EPA is embracing online community building (media wiki experiment) and mashups to foster collaboration from non-agency folk. I'm writing from the EPA Office of Information Technology Conference in St. Louis, MO. It's Nov. 15 at 8:30pm and I've just seen the future. Or at least what I hope is the future. This year's OEI conference is all about sharing. Sharing thoughts, information… knowledge. The theme was driven home by EPA's CIO, Molly A. O'Neill, at the plenary. It was then eloquently promoted by the Former EPA Administrator Bill Ruckelshaus (now Chair of the Puget Sound Partnership Leadership Council) who gave a virtual keynote. Then the experiment was announced.

The core of the experiment this week is a temporary MediaWiki instance meant to support the efforts to protect Puget Sound. There are a few maps (one Open Layers, and at least one VirtualEarth) in the wiki now and it seems more are being added by the minute. The wiki was primarily populated by conference attendees learning to wikify their knowledge. But then something magic happened. You. It seems the public found out about the experiment, perhaps through the blogosphere, and started making posts in the wiki. This was very very exciting.

I must say that the theme of online collaboration, virtual community building, and effective use of interactive technology was effectively and energetically carried throughout the conference in the booths, the sessions and in the conversations in the hall. Perhaps more importantly, no attendee could possibly leave this conference without having at least a basic understanding of how common Web collaboration concepts work, the terms associated with them (if I hear 'mashup' again I'm going to scream), and most importantly the power to combine the knowledge of The Community into something much more powerful than the sum of its bits.

I think this kind of openness by a federal agency is unprecedented very much welcomed by just about everyone I talked with or overhead. Beyond that, from working in the environmental consulting and outreach community, I know these kinds of national-scale tools for building virtual communities of practitioners and the public are sorely needed. It will help everyone learn from others in a more rapid fashion and therefore leverage targeted investments made in data, education, outreach, science, problem solving policy, etc. and multiply the extent of their reach. This extension will increase the effectiveness of those dollars and amplify their effect (we hope).

I sat with Molly tonight at the internet café as we explored the blossoming wiki and we were astonished at the volume of posts in the wiki in just 24 hours of being live. Clearly the experiment was a success.

It's a temporary thing, but I'm interested in telling EPA that the environmental community needs this service.

For more information, please see the Challenge wiki at:http://pugetsound.epageo.org

A Fluid Grid

It's true

Free citation managers

Some notes about MySQL configuration

Some notes about MySQL configuration

Even More Mercurial: sub-repos

Even More Mercurial: sub-repos

Even More Mercurial: sub-repos

More Mercurial Reading: Shared Repositories

A version of change

I've been waiting for..

Post-pre - Pre

Spatial DBs and Jumping Java

ESRI Dev Summit Keynote: SOAP vs REST

Move to the cloud

When your background data don't change

Notes from Fee

Eat your planet

EPA's Experiment in Community Building