doug-swisher.net

September 1, 2008

Bioinformatics – BioJava and C#

Filed under: Bioinformatics — Tags: , — Doug @ 10:36 pm

I stumbled across the Bioinformatics Group at the UofM, and realized that I met the president at a birthday party for a mutual friend a few months ago.  I may have the opportunity to contribute to a project or two in the coming semester(s), so I started reading a bit about bioinformatics (again).

I went looking for some code, and found a framework called BioPerl, which seems fairly popular.  My perl skills have atrophied over the years, and when I found BioJava, I was a bit more excited.  It provides a number of useful functions, and seems fairly active.  There is also a related database project, BioSQL, that both BioPerl and BioJava (along with BioRuby and BioPython) have incorporated language bindings.  BioJava even uses Hibernate as its O/R mapping layer.

Since I like to work in C#, I started playing around with porting BioJava to C#.  It’s a huge project, but it’s also a great way to see how BioJava is put together.  I’ve managed to get far enough that I can transcribe DNA to RNA using the following code:

        private static void TranscribeDNAtoRNA()
        {
            try
            {
                //make a DNA SymbolList
                ISymbolList symL = DNATools.CreateDNA("atgccgaatcgtaa");

                Console.WriteLine("DNA: " + symL.SeqString);

                symL = DNATools.ToRNA(symL);

                // just to prove it worked
                Console.WriteLine("RNA: " + symL.SeqString);
            }
            catch (IllegalSymbolException ex)
            {
                // this will happen if you try and make the DNA seq using non IUB symbols
                Console.WriteLine(ex);
            }
            catch (IllegalAlphabetException ex)
            {
                // this will happen if you try and transcribe a non DNA SymbolList
                Console.WriteLine(ex);
            }
        }

When run, the output is:

DNA: atgccgaatcgtaa
RNA: augccgaaucguaa

Yup.  A few dozen classes and a few hundred lines of code, and I can replace t’s with u’s.  Pretty exciting, eh?

Actually, I think it is pretty cool.  I’m pretty close to having the code working that will let me translate the RNA to a protein sequence or form the complement of a DNA strand.  Not rocket science, but I’ve only begun to tap the surface.  The framework allows reading sequence files (BLAST, FASTA), edit large sequences (efficiently), do pairwise alignment, and a whole lot more.

If you’re curious, you can compare the above C# code to the original Java code, which comes from the BioJava cookbook.

August 28, 2008

Robin Williams demonstrates the Spore Creature Creator

Filed under: Games — Doug @ 7:34 pm

A funny video of Robin Williams demonstrating the Spore Creature Creator.  It’s been around a while, but if you like Robin Williams and/or spore, it’s worth watching.

Less than a fortnight until Spore!

Filed under: Games — Doug @ 9:41 am

It’s now less than a fortnight (which is 14 days) until Spore hits my doorstep.  Amazon says I should receive it on the 9th of September…just in time for the second week of school.  Oh well.

The self-proclaimed “Spore Supersite” (xspore.com) has a link to a review in the Australian magazine PC Powerplay.  It is a print magazine and someone scanned the article and created a PDF, but it contains nice screen shots and artwork.  The reviewers gave it 9 out of 10 stars after playing the full game, so they must’ve liked it.  Here is the summary from the end of the article:

Pros: Limitless custom content, varied types of gameplay, no more Sims #11

Cons: Not deep enough, all about the Creators, designed for non-gamers

I haven’t been able to find any new videos, so here is a look at the game from E3 2006.  If the game looked this good two years ago, they must have spent a lot of time tweaking and refining the game play…

August 24, 2008

User Interface Design Patterns

Filed under: Software — Doug @ 2:31 pm

I stumbled across a site that has a few user interface design patterns – something I had not seen before, but which seems like a great idea.  I did a search, and a couple of sites containing web-based patterns, including Yahoo’s design pattern library, welie.com and ui-patterns.com.  The search also turned up an O’Reilly book by Jenifer Tidwell called Designing Interfaces: Patterns for Effective Interaction Design that I may have to add to my library.

On a semi-related note, I found that Joel on Software has the first few chapters of User Interface Design for Programmers online:

August 20, 2008

Genealogical Record Keeping Systems

Filed under: Genealogy — Doug @ 11:02 pm

Thinking about the user interface for my genealogy program, I thought it would be good to take a look at some of the existing record keeping solutions, as that is where I’ll be starting.  The record keeping systems allow you to store evidence, but do not include lineage-linked views.  In other words, you can store census records, birth certificates, etc., but you won’t be able to display a pedigree from them.

Here are some very quick overviews of what I’ve seen after playing with each one a few minutes each.

Clooz

Clooz is a package I’ve mentioned before, as it was the one package I had used briefly (years ago).  There is a list of object types (census, people, buildings, sources, research log) down the left side and a list view on the right side.  There is a centralized list of people, and adding a census entry consists of adding a census record and then linking folks into the census record.  All data entry is done in dialogs, making it easy to get a handful of dialogs open at the same time (census record dialog, link people dialog, add person dialog).

Clooz 2.1 Screen Shot

Clooz 2.1 Screen Shot

The Clooz home page describes the package as follows:

Clooz 2.1 is a database for systematically organizing and storing all of the clues to your ancestry that you have been collecting over the years. This is not another genealogy program. It is an electronic filing cabinet that assists you with search and retrieval of important facts that you have found during the ancestor hunt.

It uses an access database behind the scenes, and has some integration with Legacy, but that only works with version 6, and I’ve upgraded to version 7.  There is a free download on their site, limited to 29 days or 15 launches.

Custodian

Custodian is a program I hadn’t seen before.  I found it somewhat by accident in an article that contrasts it with Clooz.  Similar to Clooz, it has a list of object types down the left, but it is an MDI application, so when you go to add new items, a child window pops up, which is a big list view with buttons down the side.  Most data entry is done right in the list view, until you get to something like a name, which requires editing in a dialog.

Custodian 3 Screen Shot

Custodian 3 Screen Shot

The package is very colorful, using lots of backgrounds and shading, which I found made it hard to read at times.  The data is stored in password-protected access database files, under Program Files, of all places.  There is a free download on their site so you can try it before you buy.  The trial limits data entry to ten records per section.

Bygones

I found a link to Bygones on Cyndi’s list, which has a section for these types of packages.  It has an interesting look, in that it appears to be a piece of paper.  I found that made it a bit hard to know where to enter data.  It is written using FileMaker Pro, but I don’t know if the look is typical.

Bygones 0.9d Screen Shot

Bygones 0.9d Screen Shot

Their home page has a handful of slide show tutorials, which I probably need to watch, as I wasn’t quite sure how to use the package.  I did watch the first half of the introductory slide show, and it looked interesting.

It is a free download as a self-extracting zip, with no installer.

GenScribe

GenScribe is a Mac program that appears to be closer to what I had envisioned, in that it displays a nice representation of a census record.  The opening screen is a list of buttons for various operations.  It has a list of work to be done at a specific venue, source records, and index records.

GenScribe Census Screen

GenScribe Census Screen

I’ll have to fire up the Mac I have on loan from work and experiment with how they do the data entry.

There is a free trial download, and the full product only costs $12.

Summary

I’m not sure if I’m really qualified to make any summary statements after just a few minutes of playing around, but I’m going to do so anyway.

My impression is that these packages, in general, suffer from the same problem as lineage-linked packages, in that they don’t adequately differentiate between evidence and conclusions; they just do it from the other end of the spectrum.  For example, in Clooz, you link individuals in your database to populate specific census records.  Well, what if the person named “John Doe” in the census isn’t really the same “John Doe” you have in your database?  This can be seen below, as the “Person” dialog has a list of the census records to which the person has been linked.

Clooz Person Dialog

Clooz Person Dialog

My goal is to enter census data, birth certificates, and the like nearly verbatim so that the viability of the census record is intact, even if the person isn’t really part of my ancestry.  I should be able to link and unlink evidence and conclusions without “touching” the evidence at all.

Will I really be able to pull it off, and put together something that works better than these packages?  Probably not, but I hope to at least learn a lot along the way.

Trying to move forward on my genealogy app

Filed under: Genealogy, Software — Doug @ 7:42 am

I’ve been a bit stuck on the genealogy project, for a couple of reasons.  First, I’ve been spending a fair amount of time watching the olympics, which hasn’t left much time for coding fun.  Second, I’ve only been playing a bit with a domain model, and domain driven design just doesn’t quite feel right for this project.  It’s probably my lack of experience with the paradigm, but it seems more applicable to complex business models (lots of interactions and state changes) than it does to a single-user data repository.  I don’t regret spending time with it, as I’ve learned a lot, but I think I need to try a new tack.

Yesterday, I attended the Minneapolis Silverlight User Group meeting, which reinforced the fact that WPF is very cool, and I should probably try to use it for this project.  I played around a bit last night with Family.Show, which is a very cool, glitzy app, but it doesn’t even allow entry of sources.  (It’s a WPF reference app, and in that it succeeds very well, but it’s a long way from a full-blown genealogy app, and they readily admit that.)

My new approach is going to be to get something working, include plenty of unit tests, refactor mercilessly, and try to do the simplest thing.  I’m curious to see where that will take me.  The first thing I’m going to implement is the ability to store 1880 US Federal census records.  I know I want to use SQLite, so I’ll be using that out of the gate.  I’ll likely wind up using NHibernate as well, but I’m going to hold off adding it until I get something working (I’ve never used it, and I’ve got enough new things to learn).

I’ve only begun to explore WPF, so I’m sure the first incarnation will be ugly, smelly code, but hopefully I can refactor it into something decent.  In the very first iteration, I’m not even going to try to maintain a clean separation of concerns; I’m just going to hit the database directly, which will make writing unit tests nearly impossible.  That will be one of the first things I’ll need to fix.

Initially, the app may look and feel a bit like a WPF version of Clooz, but before I get too far, I’ll want to start hooking the evidence to the conclusions to fully realize the design I laid out in my previous post.

August 18, 2008

More Spore Videos

Filed under: Games — Doug @ 1:24 pm

Looking for spore content again over lunch, I came across some nice video’s that I hadn’t seen before, from SporeMasterRob on YouTube.  There are very nice versions of the E3 demo in four parts:

He has a handful of other videos.  I haven’t watched them all yet, but based on the first four minutes of the first video, they are well worth watching.

Only 19 days left until the game ships here in the U.S. (according to SporeWiki).

Domain-Driven Design Sample Code/Projects

Filed under: Domain-Driven Design — Tags: , — Doug @ 7:23 am

Ben Scheirman has a series of articles on developing an NHibernate application using domain-driven design:

The source code for the book .NET Domain-Driven Design with C#: Problem-Design-Solution is available online at CodePlex.

An article titled Attribute-flavored Domain Driven Design at CodeProject.com includes the source code for a naked objects-like implementation of a domain model.  A fairly bare-bones implementation like this might be an interesting place to start building my own GUI.

David Hayden talks a bit about using the Active Record pattern in DDD in his Domain-Driven Design Using Active Record in .NET article.  He also talks about application layering in Domain-Driven Design – Layered Applications, which refers to some sample code for a shopping cart.

August 14, 2008

Only 21 days until spore comes out!

Filed under: Games — Tags: — Doug @ 1:14 pm

I’ve been eagerly awaiting the release of Spore, the new game by Will Wright.  While eating my lunch, I came across this cool video, which gives a nice overview of the game, and then shows some details of the first phase of the game.

I pre-ordered my copy almost a year ago.  It should arrive the first week of September.  I can’t wait!

August 11, 2008

Articles on Project Organization

Filed under: Software — Tags: — Doug @ 7:33 pm

This post just contains some links to other articles that include ideas on how to structure the code and build artifacts for a project, along with sample projects that use domain-driven design.

Scott Hanselman: How do you organize your code?

Mike Roberts (author of TreeSurgeon) has a series of articles on development tree organization:

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