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Big things coming or maybe not

1/10/2005

A week without much happening on this site, but plenty of things happening on the background. Thus, no posts but plenty of emails and me quite busy and dealing with ‘should I go for the next big thing or not?’. Decisions, negotiations, decisions…

Some interesting things that I have seen:

  • Dick Hardt’s presentation on Identity 2.0 nicely done, good overview and very entertaining.
  • I have installed the Web Developer extension for Firefox. It is a very nice tool for debugging CSS styles for web pages, and I do need to clean up the styles of Plus Tree, Quantum Forest and the Wiki part of this site. Have a look at The Tao of Mac for a good list of Firefox extensions.
  • I have posted a few new words to the Alpha Agora, including hypergraphia, slapstick and bahuvrihi.
  • Quote of the week (follow the link for a .wav file with that part of the movie):

Ah-Ah, I know what you’re thinking. Did he fire six shots or only five? Well, to tell you the truth, in all this excitement, I’ve kinda lost track myself. But being as this is a .44 Magnum, the most powerful handgun in the world, and would blow your head clean off, you’ve got to ask yourself one question: ‘Do I feel lucky?’ Well, do ya punk?—Clint Eastwood in Dirty Harry.

This weekend is family time and helping some friends with a bunch of cows: it does not get more removed from the web than that.

Cows and us

Filed in miscellanea, quotes, web 1 Comment

Moving site to Pmwiki

23/05/2005

I have been thinking about this for a while and I have decided to move most pages on this site to a Wiki1. I do not mean the Quantum Forest weblog, which lives happily in Textpattern, but the rest of the ‘static’ (not generated ‘on the fly’) pages.

I would really like to have a system that combines wikiness and weblogging, but I have not found a nice implementation. I would really like to have a Wiki that implements Textile, but I as far as I know only Instiki (a Wiki implemented in Ruby) does it at the moment, and I do not have the privileges to install it in my system. Thus, soon I will be moving all static pages to PmWiki.

Supposedly, the biggest problem would be to transform all the HTML to PmWiki markup, but I found the HTML::Wiki Converter, which does a good job moving HTML not only to PmWiki, but to:

The other issue is to redirect the old pages to the new ones, without risking losing Google (and other search engines) rankings. I will follow Google’s recommendation and use a 301 redirect, as explained here.

On top of using a ‘plain PmWiki’ implementation, I am thinking of using ‘clean URLs’ (which require these changes), user authentication (with this plugin), and extended markup (with this other plugin). The latter until I can get Textile working in PmWiki.

I will not be posting much here until I finish creating the templates, transforming content and redirecting the old pages to the new ones.

1 A previous post considers moving only the ASReml Cookbook, but I guess it is better to move the whole site now.

PS. 2005-05-31. The HTML::Wiki Converter has a few hiccups missing a few anchors inside pages and the notation for subscripts and superscripts misses the inverted commas.

PS. 2005-06-10. It took ten days for Google and Yahoo to replace the old addresses with the new ones, so the permanent redirect did work. There was a period of three days when Google was showing both the old and new addresses in search results.

Filed in software, web, writing No Comments

Intellectual bullying

16/05/2005

I am a big fan of Splus and R and I am often recommending these systems to colleagues. One of the many reasons I like the programs is their very active users’ communities. If one runs into trouble, there are always other users willing to help. Nevertheless, a while ago I started noticing a disturbing trend: one of the Splus/R language demigods was becoming increasingly arrogant—and rude—in his replies to fellow posters. What was even more surprising is that nobody seemed to care. As Eric Hoffer said:

Rudeness is the weak man’s imitation of strength.

I was uncomfortable, but the situation was below my ‘annoyance threshold’ until this reply to this post. I was so annoyed that submitted this message, which generated an interesting discussion that resulted in a ‘lawyer-style’ apology from the offender. The interesting thing is that—after my post—I received several personal emails from people that where equally uncomfortable with the situation, but felt uneasy challenging the ‘powers that be’. This seems to be yet another example of the issues faced by internet communities, where a few individuals can easily damage the quality of communication in a forum.

I think that after this experience we will go back to a much more respectful and welcoming email list, so people are not afraid of posting simple questions and being flamed in the process.

Filed in quotes, statistics, web No Comments

Playing with Google tools

25/04/2005

During the last ten years there have been few changes in the way we use computers. Almost everybody has moved from ‘console like’ interactions to GUI, but the way we treat information is pretty much the same. The web added new text files but we kept filing them in a similar fashion.

Google was a welcome addition to the growing list of search engines, but it did not change the way I would look for information. It just improved it through making the results more relevant and a terser interface—a welcome departure from the old ‘information portals’. However, Gmail (Google mail) has changed the way I use email; not at work but at least for my private addresses.

I have disposed of hierarchical folders and just ‘archive’ mail, some times attaching labels (keywords, tags, whatever word you may prefer). I still delete email, despite of Gmail’s suggestions, mostly due to me following GTD. I have now set up my Gmail account as a ‘catch all’ address for all my personal email addresses (around five or six of them).

Gmail already features integration of simple rich text format in documents. This could easily open the door to the creation of simple documents (which include most of the content creation normal people do) in addition to emails. Of course this would not satisfy ‘power users’, but would be more than enough for the majority who never uses equation editor, sections or even styles. Spell checking can already be provided by browser plugins (e.g., SpellBound—the spell checker not the movie). Other plugins could provide support for text editing with syntax highlighting for the programmers out there.

Apart from a good interface the other feature is the shear amount of disk space allocated to users. With 2GB I already use my email account for basic synchronisation of my computers at work and at home. It is just matter of emailing myself the attachment. From that basic usage to proper synchronisation it should be a small step.

Blurring the barriers of search

The second Google product that has started to change my habits is Desktop Search. The structure of my hard drive contains a huge number of hierarchical folders (with five or six levels of nesting), in an attempt to keep data organised in a meaningful way. Of course I often tend to forget exactly where is a particular piece of information. Desktop search extends the Google interface to my computer, indexing the most common file formats1. If I can not remember where I put the PDF file discussing the use of ConTEXt I just type ‘context latex filetype:pdf’ and the file is at the top of my search.

The idea of getting rid of the hierarchical structure is not new. I used before The Brain and tried Life Streams, but I find the search engine interface much more convenient. The Brain had a ‘cool looking’ interface, but it was not as easy to use as Google Search. Life Streams used time as interface, but I tend to remember keywords and file types over when I was actually doing the work, particularly for long gone projects.

I would love to know what other products Google has in the pipeline. Already including search, email, pictures and blogging—and with the possibility of easily including basic word processing—Google is looking more and more as a competitor of Microsoft’s desktop dominance. In fact, it probably would not need to directly compete with Microsoft, but only to side step it. Microsoft would still dominate the business user’s market, which tend to use more features and would be less inclined to put files in Google’s hard drives.

Nevertheless, Google could offer Gmail to small businesses, allowing them to have a similar interface but putting their logos and using their domains instead of Gmail’s. I would love to use something like that with my own domain name. Large corporations are still too keen in ‘collaboration software’ with invites to meetings and booking rooms and silly things like that, which would not be difficult to implement but would add clutter to the clean interface.

Anyway, many home users would have enough with Google tools, so why would someone pay for MS Office for typing letters? What would you miss as a home user? May be a simple spreadsheet, nothing complex, but an array that supports simple mathematical operations (even some financial functions). I guess that it would be possible to have something like ‘Google Calc’ and say bye to Office.

1 In fact there are already plenty of plugins for this product. Because desktop uses file extensions to identify file types, it may miss some less common extensions. There is already a plugin that lets the user to specify additional extensions for text files (Larry’s Any Text File Indexer) . I used it to include my .tex (LATEX) and .as (ASReml) files.

Filed in software, web No Comments

Kick-starting plus tree

6/04/2005

This post represents the first official reference to Plus Tree, the site that will support most of my genetics and breeding work. I know, the site is not yet ready for prime time, but I think it has reached a state of ‘potential usefulness’ for people interested in the topic.

I will try to post short essays around once a month, but there are no guarantees. A friend of mine asked ‘Why are you giving away that stuff for free?’ The simple answer is because most posts do not represent ground breaking ideas; however, the fact is that they are rarely implemented in breeding programs — particularly in a single program. In addition, imagine what you would get if you actually pay me to do some work!

In the not so distant future I will make available a couple of features that I am still testing for the site, including access to open projects — or at least the basic ideas behind them — as well as (probably) a Wiki system.

Some people know that I have been looking from the sidelines of genetics for a while. Let’s say that now I am starting to play again: slowly but steadily.

Filed in genetics, web No Comments

Wikis and information management

5/02/2005

There is a lot of project information, ideas, and not really structured information that I find hard to store. As I work in projects with people overseas (with whom I have no direct contact in many cases), the idea of an easily up datable site, where to put my (and their) current brain dump is very appealing. I am playing with the idea of transforming my ASReml cookbook into a Wiki site that can be corrected and improved by other ASReml users.

There are plenty of Wikis to choose from, and I have been playing with PmWiki, a Wiki clone written in PHP. I would prefer a Wiki clone written in Python (so I can tinker with it), like Moin Moin, but I not seem to have the administration privileges to set it up properly in my web server.

Wikis are collaborative sites by definition, but I want to limit access to people really knowledgeable in ASReml, so I will need to password protect the site (to avoid annoying modifications by spammers).

Log to self: Trac is an interesting Wiki for project management (with a subversion back end). This could be a good choice for software projects.

Filed in software, web No Comments

Lively conversation and internet communities

9/12/2004

We had some wonderful conversations with Peter in Wakefield, New Zealand (map). We were talking about the links between optimism and optimum and later Peter was telling me about the relationship between adventious events and religion. Then he mentioned the connection between Chrestos (sense auspicious, good) and Christianity. The word chrestos sounded familiar to me, when I remembered the word chrestomathy (a selection of literary passages).

Luis, Orlando and Peter in Pitfure House, Wakefield, NZ

While we were talking about the etymology of these words I mentioned that I thought there was a name for words of mixed etymology. I could not remember the word, and the closest I have got is to macaronic (yes, it sounds like pasta). Do you know the word I was thinking of? If you do, please contact me using this form. This is just another case of loganamnosis.

Sadly, my problems to find the word relate to the disappearance of The Agora (following the link you may get a ‘page not found’ error message). It is hard to create a vibrant internet community and it is so easy to destroy it. First it was the electronic implosion where there were thousands of posts lost. Then another minor implosion and then total disappearance. A real shame.

P.S. 2004-12-10. The Agora seems to be working again…

Filed in language, orlando, web No Comments

Prototyping breedOmatic

28/09/2004

This weekend I was working in my latest project — codename breedOmatic — writing a Python script to process the information obtained through a web form. I started working directly in the “production machine”; however, with a lousy internet connection the development and testing process was really slow.

I decided to use IIS (Internet Information Services) in my laptop — I am running windows 2000, but I discovered that it was not available. As an aside, at work machines are always setup in a very limited, barebones, way. Then, I needed to download a very small server (so I had some hope with my connection). Here comes TinyWeb, a wonderfully small (53KB) free web server by Ritlabs. I also installed TinyBox, a free controler for TinyWeb. The couple of programs work very well.

In a previous post I mentioned that I would give a try to JEdit, a java based text editor. Well, I installed it and I have had a great experience using it; and I am writing this post with it. Tip: if you are going to be using HTML or XHTML some very useful plugins for this editor is the XML plugin. There are some dependencies though, so you also need to have two other small plugins: Sidekick and ErrorLine.

P.S. 2004-09-28
1. I found a bug in JEdit, printing to networked printers under Windows 2000.
2. Note to self: the first line of a Python script needs to contain #!c:\python23\python.exe to be ran in a windows server.

Filed in programming, software, web No Comments

Copyright and rights management

30/06/2004

I read a very interesting presentation to Microsoft’s Research Group by Cory Doctorow on Digital Rights Management (DRM), and why the technology does not make any sense. By the way, Cory works for the Electronic Frontier Foundation, an organisation that aims to “defend freedom in the digital world”. It was a quite coherent and well presented argument, going point by point on the lame excuses used by people that want to control content.

The presentation made me think a bit more on how I do make available the contents of my web site, basically about copyright. The contents of this site are available under three different copyright agreements:

The latter license is the most liberal, and allows you to do any non-commercial activity with the material, except claim that you wrote it or designed it. Any of the conditions can be waived if you get my permission as copyright holder.

As a researcher, I am always keen on making the results of my work freely available. In fact, I am now favouring publication in journals that respect my right to make copies of my work freely available to colleagues, for example the Canadian Journal of Forest Research (with some limitations so they can make a buck). Meanwhile, I am busy uploading PDF files for all publications for which I have the right to distribute copies (luckily that includes most of them). The rationale behind my decision is that I am using work by other people as the basis of my own work, so the decent thing to do is to allow others to use my work. I still may have to sort out ways of convincing my employer that this is the best course of action, but I am convinced that that is the case.

Incidentally, this is the last post for this financial year. Better I finish shopping so I can claim everything in my next tax return. As the Angry Economist points out “you may ignore Economics but Economics won’t ignore you”.

Filed in miscellanea, web No Comments

Testing design under different browsers

8/04/2004

Since I moved “quantum forest” from Greymatter to Textpattern I have also been changing and tweaking the new design, or rather my modification to the default template. One of the problems I have is that I can only test the pages in my computer running Microsoft Windows — using Internet Explorer and Mozilla Firebird. However, checking the logs of my server I can see that there is a small percentage (from 5 to 7 percent) of visitors that use other browsers. They are a small group, but a sign of minimum consideration is to have pages that can be properly read by any browser.

Thus, I had no Macintosh and no friend with a Macintosh… The solution for me was to find a great service that emulates Safari, one of the popular browsers in Apple computers: iCapture. One just enters the URL to render, comes back in 30 seconds and there is a picture in PNG format of a screen capture of the site as seen in Safari.

I can only say thanks — actually, I should donate something — to the programmer of such a simple and useful system. Even better, the system was partly programmed in my favourite language: Python. The author even shares my good taste in programming.

P.S. Since 2005 I have used a mac at home and since 2006 one at work too, so no need for the web site.

Filed in web No Comments