Quantum Forest

A few days without posting but first I was away in mighty Timaru and then my laptop underwent some serious upgrade. I will write about the latter here.

I have been using Parallels for a while, but despite all the good press I still find it painfully slow. I tend to use the windows side of things mostly for two things: scientific software (SAS, ASReml and arcGIS) and Quickbooks (cashbook for consulting income). The first category is very demanding on memory and disk space, while the second is just buggy and poorly written, but it works with what my accountant needs.

While I am using the programs under windows I am rarely doing something on the mac side of things. Thus, I think I am better off with dual booting for the few times when I need Windows in my laptop. Given that I was going to have to save all the data, partition the disk, etc. I also used this time for upgrading to Leopard (OS X 10.5) as well. I also upgraded to iWork 08, so I can waste only one day to have the laptop ready.

After a few configurations hiccups (mostly negotiating things with the network) the laptop is performing quite well. Windows XP runs very fast: in fact, faster than in any other laptop that I have used in the past. This afternoon I will install software on the XP side of things.

I do not like much writing with a white background (my eyes hurt). Therefore I have changed the default colours for TexShop’s editor using the following commands in a Terminal window:


# These lines change background colour (in RGB proportions)
defaults write TeXShop background_R .1
defaults write TeXShop background_G .1
defaults write TeXShop background_B .1
# These lines change the font colour for comments
defaults write TeXShop commentred .99
defaults write TeXShop commentgreen .96
defaults write TeXShop commentblue .90


It is also possible to change transparency of the editor window with something like defaults write TeXShop SourceWindowAlpha 0.85.

I am in the process of obtaining a visa, for which the application requires a 3×4 cm picture. I have a couple of good ‘passport type’ pictures; however, it is not possible to print passport size (or small size, for that matter) pictures from either iPhoto or Picasa.

There are a few products for either mac or windows that let you print these small sizes. Nevertheless, why would one pay for adding barebones functionality to software? http://www.epassportphoto.com allows choosing country and type of document (to get the exact size required), and then uploading a picture. The picture is then resized in such a way as to get the right photo size when printing in common photo paper.

This is the only function of this free site and it works really well.

I decided to use a Google Earth flyover video in my first FORE111 lecture (Trees, Forests and Environment) this coming Monday. When I first read that this was possible I did it without paying much attention. After preparing the route for the fly over different types of forests I realised that recording movies was a feature of the professional (meaning US$400) version of Google Earth.

After the initial shock, and immediate decision not to fork out US$400 for three minutes of lecture, I had a quick look at the options. Of course I tried a freebie (Copernicus), but did not get anywhere in terms of results (the program kept on crashing). I then tried and bought iShowU — made by a New Zealand company — which showed to be easy to use, created reasonable sized video files and cheap (US$20 + GST).

If the flyover works on Monday I am hoping to create a few more for later during the semester.

For some bizarre reason, in the last week I have become very popular as referee for journals, Ph.D. theses and industry reports. I am in need of seriously streamlining my workflow these ‘for the good of science’ type of activities, because I can allocate only a fairly limited time to them. Thus, I need:

1. Something that reads PDF documents (all documents that I am receiving come as PDF).
2. Hopefully no printing involved, because there is no much point on keeping around copies of draft documents.
3. Full screen, so it is easy to read documents and avoids distraction.
4. An easy way to keep track of annotations.
5. Cheap, remember that this is for the good of humanity.

A quick web search pointed to Skim, which fits the bill in all points (including the last point: free). There are more powerful applications (like the full version of Adobe Acrobat), but I can not see the point of the expense. A nice (30 euros) alternative is Papers, which in addition of facilitating ’studying’ or reading from PDFs, it is quite good at organising PDFs. Last time I checked the program it could only search and import documents from PubMed (in addition to local documents). However, it seems that now it also works with Web of Science (that I use the most), Google Scholar (which I rarely use) and a few others.

So, the way things work now when I am refereeing is:

1. PDF is read in Skim.
2. Notes are directly inserted in Skim.
3. Type my comments to the journal in TextEdit in rich text format (RTF). This is to avoid wasting time tweaking the document. I still used Word for writing papers and reports.
4. Print and mail a PDF version to the journal.

And that’s it. It certainly makes things a lot less painful for me.

There has been a proliferation of writing software, with many of the packages striving for recapturing simplicity lost long ago. We complain about distractions, but use tools that are designed to do many different (and non-essential) things at the same time. If I go back at my DOS times (second half of the 1980s), a computer would do one thing at the time: if I needed to write a document I would use Wordperfect, for a spreadsheet Quattro Pro, etc. It was not possible to use both simultaneously. There was no email, internet connection or music at the same time.

We are now like spoiled children: there are too many things claiming for our attention, but we can not turn them off. We are hooked into a permanent attention deficit disorder because we choose so. Then, we long for a tool that will fix our distraction but, maybe, we could just use programs maximising the windows (to fully occupy the screen) and, to avoid temptation, turn off our network connection.

On writing software

A big component of my work is writing documents. In my mind there is a clear distinction between the solitary endeavour (where I can use whatever software I like) and the shared document (with a large number of compromises). I do not have problems with Word as bloated software, because I use many of the non-basic (aka bloat) features: equations, footnotes, crossreferences, citing using referencing software (like Endnote), table of contents, tables, indexing, tracking changes, etc. However, I do have issues with stability (or lack of it), particularly when dealing with long documents.

I have had a look at several alternative programs, but none of them have enough mind share as to make it a reasonably popular alternative. Using something like LaTeX would probably cover most (if not all) of my needs. However, I do not work with anybody that has a clue about using LaTeX, and nobody has the time and inclination to learn about it. Yes, it has the advantage of working with plain text files, but it is huge (larger than Word) and there is no standard way of dealing with the revision process, short of installing a versioning system.

Other wordprocessing systems that do what I need are equally ‘bloated’: OpenOffice and Mellel have all the ‘distractions’ and, again, they are not perfectly compatible with the standard. Then, their only advantage is that they are cheaper than Word. Nevertheless, most people already paid for Word, so it is a sunk cost. Thus, the sad reality is that Word is a de facto standard.

At the end of the day, Word is good enough and there are no compelling alternatives. However, I do use other tools for writing early drafts to get the ball rolling. Once I have the basics I move the text to Word. So, what are the basic tools? Some times I use TextWrangler (free) or Journler, depending if I want to store the information in an individual file or don’t worry about that and leave it in a database.

I guess that if one is motivated enough, one can find nirvana even in Word — granted, with some work involved.

As soon as I heard the news of Google Calendar I got really interested in the idea. As many other people, I found the service quite interesting but with three annoying missing features:

1. Option to set calendar hours, I mean start and finish hours for a day. I rarely make appointments at 3 am or 11pm. This makes life easier but one can live — at least for a while — without this being implemented.
2. Simple to dos, with keywords (tags) and due dates. This one is important but, again, I can wait for this or keep my list somewhere else.
3. The ‘almost a deal breaker’: lack of synchronisation with desktop clients (iCal in my case). How does one access the bloody calendar without internet access and/or a supported browser?

Spanning Sync has positioned itself almost as the de facto synchronisation product between Google Calendar and iCal. However, I still struggled with its price: USD25 per year or USD65 for a permanent subscription sounded very steep just for syncing; particularly when using Google Calendar is essentially free.

I then tried a couple of other approaches. I tested using Thunderbird + Lightning + Provider. I do not mind using Thunderbird as an email client: I think it is quite good, except for the lack of integration with Address Book in the mac. However, after following a very good description of the setup, I realised that the calendar is synchronised and visible only when there is internet connection, defeating the purpose. I am sure the developers are working in persistence while disconnected, but meanwhile is essentially useless.

Quick note here: Incidentally, if you have problems adding a second calendar, just use your normal login and password for the calendars, rather than the bigcode@group.calendar.google.com set up by default.

After not making progress with Thunderbird, I went for GCALDaemon. After fiddling around with download, permissions, editing configuration files, etc. I managed to make it run. Nevertheless, it crashed and trashed the contents of my online Google Calendar after one hour of use. Good thing that I had a backup. I can’t remember where I read a user commenting that ‘why would you pay for Spanning Sync if there was GCALDaemon’. Short answer: read the previous three sentences.

At some point, one realises that the time invested (or wasted) is certainly worth much more than the syncing service’s cost. So I was ready to pay for Spanning Sync, when one major improvement was announced: mobile browser access (http://mobile.google.com/calendar). I always carry my mobile phone, so if I have coverage (most of the time) I am OK. When visiting Australia last April I could still access Vodafone at domestic prices, making the system viable. However, when roaming in other countries the price to access calendar and email through the phone quickly becomes prohibitive. A good thing is that this type of trip does not happen that often, so I will rely on mobile access for the next couple of months and give the system a proper test.

I spend most of my work day in front of a computer. Thus, having a reasonable setup is very important. I use a fairly clean mac, with a few add-ons. I tend to work a lot with standard mac software (meaning that came with the macbook pro). Thus, I use Safari for browsing, Mail for email, iCal for appointments, Address Book for contacts, iTunes for music and iPhoto for pictures. One of my favourite things is the high level of integration between the standard software. At work the IT department installed Entourage, Firefox and Thunderbird just in case I wanted to use it but:

1. I had a short lived love affair with Firefox, but it still did not feel quite right as a mac program.
2. I could not stand the ugliness of Entourage, although I understand that some people like to have everything in one program.
3. Thunderbird felt quite responsive compared to Mail (whose IMAP support is not great), but it did not use the standard Address Book, and I dislike entering information more than once.

Of course this software setup does not cover everything that I need to do, so I use a few other programs too:

1. Keynote feels much better for presentations than Powerpoint. It is more elegant and the themes look much better that anything PowerPoint brings by default. Keynote is one half of `iWork and I have to say that I do not like Pages (the other half), which is slow as hell.
2. Yep to classify my PDF files. It is by far the simplest and most efficient solution. Through work I have access to Endnote, which is clunky and far less visually appealing. I am not sure what the pricing will be in the future (at the moment is free) but I think it will be worth the money.
3. I work in a fairly visual way: if I can draw things I can understand them a lot better. Curio is great at allowing me to organise my meeting notes, sketches, I even do some mind mapping with it some times. I can organise text in it too; certainly not as efficiently as in other applications, but it does the job. I use the professional edition.
4. Did I mention that I am an old fart (forty and counting)? I grew up with keyboard shortcuts, and I rather do that instead of mousing my way around. No sense of superiority here, it is just easier to me. Quicksilver really shines if you like working with the keyboard. If you like playing with the mouse it will not be your cup of tree.
5. Office. My excuses are that I have to exchange documents with colleagues, and Word and Excel are de facto standards. Overkill, with lots of features that I do not use and appalling graphics. However, I do like tables and comments in Word (it would nice if it included better versioning) and pivot tables in Excel.

I have also tried a few things that did not work very well for me including: Devonthink (I did not get it; I may not be smart enough to do something useful with it), Mori (I do not to like much to use a folder structure for my thoughts: things always fit in to more than one class) and WriteRoom (I use version 1 sporadically, which in my opinion was better than the second version. A clear case of when less is more).

At work I also use a PC, which has Office, Firefox and a bunch of scientific software which is of no relevance to this post. Enough to say that I spend 80% or more of my time working in the mac, which feels so much more welcoming than my PC. Sure, it is not perfect and there are a few things that annoy me — like the lack of control over compression rate in iPhoto when exporting and not being able to sync my phone with the macbook — but they are minor compared to my PC experience.

I switched from PCs only two years ago, but now I feel mostly at home. I do not like mac zealotry and mythology (which confuses consistency with intuitive), but I have been happier with my macs than with any PC in the past. Well, except for the first computer I owned, a brand-less 286 running DOS. But how do you compete with the first time of anything?

For quantitative geneticists and breeders out there: ASReml runs OK in any mac with Intel processor and Parallels. You can find some comments on using it in the ASReml Cookbook.

Incidentally, SAS works OK in a mac using Parallels too. However, I am enjoying R a lot more.

(Or why do I prefer software where I do have a say)

Recently I was commenting on some software that I use for writing. I think that one of the main reasons non-strictly related to software usefulness is the quality of the community around the software. This has two elements:

• How open is the developer to feedback from the users and
• How active is the community at using the software to push the developer(s) to continue moving forward.

As an example, I like using Journler to keep track of odd ends in my mac computer. I also like using Writeroom when starting to write, because I can focus on my ideas only. Both programs have relatively active groups of users (here and here) and receptive developers, who are looking for feedback. The feeling is of people who care about a product, which in general is a necessary (although not sufficient) condition for good programs. By comparison, I struggle with Copywrite, because there is no public feedback mechanism: I do not know what other users think or what are the projects of the developer for this software. Is he (or she) still developing it or now he is moving to live in Vanuatu to enjoy the rest of his life?

An interesting element is that both Writeroom and Journler are free (sensu gratis)—although the developers ask for donations—while Copywrite costs US$30 or so. There is a psychological element on paying for software; one thinks that the programmers must be working on the product. However, there is no feedback to confirm this assumption in Copywrite. In addition, I expect more activity from smaller companies: they are supossed to be more agile than, say, Microsoft.

Thus, if you are a small company I expect you to show some changes here and there. If you are a small company and charge for your product I better should have a say on what is going on. If you are a large company, most likely I will buy your software only if I need to, because most probably you are developing not very interesting products (there are exceptions¹ of course).

¹ Wolfram’s Mathematica is an example. Insightful’s Splus is not: R is much more active, there is plenty of feedback and it is free.