DevBioSim

New personal blog

2008-08-07T09:06:00.002-05:00

I've started a personal blog, at doug-swisher.net. I haven't decided yet whether I'm moving this blog over there or not.

WormCG

2008-07-30T07:44:00.002-05:00

I've found a number of data sources that contain cell lineage and position information for the C. elegans embryo but they are not in a common format, or they are embedded in a scholarly paper. I've started building a "data warehouse" to store all this data in a common format, called WormCG (for worm computational geometry). The design is very loosely based on BioWarehouse.

To start, WormCG will only contain cell position information. I plan to extend it to include the cell outline and other features, but I have yet to see a data source for that type of data (so I may be going through images and tracing the data).

Once I have some initial data imported, I'll begin writing some tools to pull it out and visualize it. I did a quick spike where I created a 3D volume in nrrd format and used 3DSlicer to examine it, and that seems like a good initial approach. 3DSlicer is a wonderful program, but it does not have any 4D support (or if it does, I haven't been able to find it).

The code for WormCG will be posted on the sourceforge site within a week or two.

Visualization Tools

2008-07-11T10:19:00.005-05:00

I've been looking for file formats that I could borrow, but didn't have much luck until this morning, and now I've got a case of information overload. Here is a sampling, all of which requires more in-depth reading. These aren't file formats, per se, but are visualization tools for viewing data similar to what I'll be generating, and most of them include file format specifications, conversions, and the like.

Vis5D+
I had seen GRASS's Grid3D, but did not see their reference to a visualization tool called Vis5d+. Vis5d+ is an open source project hosted on SourceForge, targeted at Unix platforms, billed as "a free OpenGL-based volumetric visualization program for scientific datasets in 3+ dimensions". Many of the screen shots are meterological data (clouds, isobars, etc), but it isn't restricted to that domain.

The file format is pretty flexible, but the preferred format is a 5D rectangle. Quoting from the Vis5D+ manual:

Vis5D can work with data organized as a 5-D rectangle. The first 3 dimensions are spatial: rows, columns, and levels (or latitutude, longitude, and height). The 4th dimension is time. The 5th dimension is the enumeration of multiple physical variables such as temperature, pressure, water content, etc.

There is a windows port called PC-Vis5D, but I haven't seen a download link, and the code appears to be a bit stale (the latest release was in 2000, if I'm reading the site correctly).

Volume4D PRO
There are a bunch of applications in the commercial space, including Volume4D PRO, aimed primarily at medical imaging (MRI, CT scan, etc). It is basically a 4D voxel visualization tool.

VisBio
The VisBio tool, "a biological visualization tool designed for easy visualization and analysis of multidimensional image data," also looks intriguing. It is aimed at visualization of microscopy data, but that includes 3D data. It doesn't appear to handle 4D data, but does provide links the Bio-Formats library, "a standalone Java library for reading and writing microscopy file formats". I have not had a chance to review all the formats to see if any of them include 4D capability.

They include a couple of sample movies, one of which is a volume rendering of a C. elegans embryo undergoing cell fusion. The movie isn't 4D data, but a rotation of a static model.

It runs on Windows, Mac, Linux, etc., and the source code is available.

VisAD
I also stumbled across VisAD, "a Java component library for interactive and collaborative visualization and analysis of numerical data". I haven't had time to fully understand it yet, but their file formats page includes Vis5D, HDF5, NetCDF, and others.

Voxels?

2008-07-08T09:30:00.003-05:00

After more in-depth study of CompuCell3D and other papers/projects, I'm thinking that the best way to represent the biological model is using voxels/cellular automata. It certainly makes some of the rendering easier, if efficiency isn't an issue. It might make some of the computation harder, though. And of course, I've not played much at all with voxels...

According to a paper entitled "Volume Graphics", voxelization refers to taking geometric objects and converting them to a voxel representation. Going in the opposite direction is referred to as volume rendering.

A number of data structures have been developed to represent volume data, including octrees and BSP trees.

Voxels (spatial occupancy enumeration) are just one form of solid modeling; others include cellular decomposition, constructive solid geometry, etc.

Lunch Surfing

2008-04-25T13:32:00.003-05:00

While I was eating a Chipotle burrito at my desk, I did a little web surfing. Earlier in the week, I found a paper titled Executable cell biology, by Fisher and Henzinger, so I thought I'd follow up. I found the home page for Jasmin Fisher, then took a look at her publications. She has one coming out in the new issue of IEEE/ACM TCBB, but it's not available online (yet).

I did some more clicking and searching, and somehow ended up on a paper by Honda and Nagai, et al, titled Computer simulation of emerging asymmetry in the mouse blastocyst. That article is interesting, but complex, so I followed the citations back in time. They published an article on their 3D vertex dynamics cell model in 2004, and the 2D model in 2001.

Looking at some of the citations, Honda has been at this a while, as some of the citations are nearly 20 years old. Some of the other citations also looked interesting, so I'll have to follow up on them one of these days.

Anyway, the 2D model looks like an interesting thing to try and implement before I try to implement a 3D model - 2D graphics are quite a bit easier.

Still here - really!

2008-04-21T08:08:00.003-05:00

School has kept me way too busy the last few months, and I've neglected this work. (Taking two laboratory classes is way more work than one lecture class, even though the credit load is the same.)

I've also been working a bit on an open source project - the Civ4 World Template Builder. I'm not sure how much farther I'm going to take that code; I'm getting close to posting a link to it on the Civ Fanatics site, and if folks are interested, I'll keep plugging away.

Regardless, I want to pull this project out of mothballs and get going again. I need to explore OpenGL a bit more deeply than I have in the past, as the code just isn't working quite right. (And besides, I'm also playing with some iPhone stuff for work, which uses OpenGL.)

While doing a bit of searching, I came across a handy site, called GLProgramming. On their links page, they have links to HTML versions of the Blue Book and the Red Book, which should come in quite handy.

My goal over the next couple of weeks is to slog through chapter 3 of the Red Book, which is on viewing. Once I've gone through that, I should be able to fix the transforms in my OpenGL code so things work properly. I'll be adding more code to the OpenGLExamples spike within the DevBioSim SF project.

Still Here

2008-01-13T10:02:00.000-06:00

It has been one month since I've posted here - way too long. Between finals, the holidays, business travel, and things breaking around the house, and some WoW, I haven't made time for the biology stuff.

Hopefully, I'll be able to get back in the swing of things and make some headway over the next few days.

Finals Week, OpenId

2007-12-13T07:07:00.000-06:00

Ugh, it's finals week. I don't have any spare time...not even for WoW.

At work, we're looking at OpenId, which looks like a cool idea. I'm working on a feasibility study to proof it out - provider in .Net, relying party in Java. Given that I've never done much Java, it is taking quite a bit longer than I'd like, but I'm getting close to having it wrapped up.

Finals will be over soon (less than a week), and the holidays are coming up, so I'm hoping to get time to work on the simulations.

Leveling my rogue

2007-12-04T07:19:00.000-06:00

I spent too much time over the weekend playing my rogue - Meemie. Leveling went pretty fast, though, and I was able to go from 11 to 17. Brizel and Neomage also formed a 2v2 arena team to start accumulating arena points. So far, we're 1-9, but hopefully we get better as we go. We also played our Warlocks for a bit, and hit 47.

I'm still trying to decide what to do with my mage to get good gear. Should I drop skinning and pick up tailoring so I can get the Spellfire set? What about engineering?

My hunter also needs gear. It seems unfair that the tailoring recipes are attainable without running heroics, but the dragonscale leatherworking gear requires primal nethers (except for the bracers).

The OpenGL examples project needs some attention. I did manage to complete one example and start another, but its not working quite right. Hopefully, I can squeeze in some time this week.

My final exam is two weeks away, so time will be even more precious.

Cell Position Data

2007-11-28T07:08:00.000-06:00

One thing that I'll need before too much longer is position information for the cells in the C. elegans embryo. I did some literature searches, and came up with a couple of papers.

The first, "The embryonic cell lineage of the nematode Caenorhabditis elegans" by Sulston, et al, seems to be the seminal paper on cell lineage, and contains a ton of information on lineage as well as cell position in the embryo.

The second, "Assessing normal embryogenesis in Caenorhabditis elegans using a 4D microscope: variability of development and regional specification" by Schnabel, et al, also contains a fair amount of cell position information. The other thing that makes this paper interesting is that it shows the variability of events during embryogenesis. This variability data will be useful far in the future to help establish a baseline against which various models can be validated.

Last but not least, I found a couple of software packages that provide views of the developing embryo. One, Angler, contains a data file in the unix version that gives the position of each cell in 4D space (3D position plus time of birth).

OpenGL Here I Come

2007-11-26T07:49:00.000-06:00

Ok, it has been way too long since I've posted. Chalk it up to exams, the holiday, and a World of Warcraft binge (I got my mage up to level 70 - woohoo!).

Anyway, I've pretty much given up on XNA in favor of OpenGL for my project. There are a couple of reasons for this.

First, I've used OpenGL in the past, so the learning curve won't be quite as steep.

Second, I'm not creating a game, so XNA doesn't fit quite right. OpenGL runs on my laptop (XNA doesn't - at least, not the examples I've tested). I'm not creating models and importing them into the app, which seems to be what XNA is tailored to do.

Third, I can run OpenGL inside a windows form, with menus and whatnot. Very handy for what I want. I found an open source control to make it trivial.

I'm not bashing XNA. If I were writing game, I'd use it in a heartbeat. But I'm not writing a game, which at least in my opinion, makes OpenGL a better choice.

Right now, I'm going through some OpenGL examples, trying to get the transparency right. The code is all in the devbiosim subversion repository on SourceForge, under the OpenGL examples spike.

Life is busy right now

2007-11-09T06:54:00.000-06:00

I've got an exam coming up on Tuesday for Cell Bio. Work has been insanely busy (long days). My daughter has had a bunch of basketball games. With all of that, I haven't had time for much of anything else...even sleep time is suffering.

After my exam, I'm hoping to get back into the devbiosim code and make some headway.

Hellgate London

2007-11-06T07:09:00.000-06:00

My son's copy of Hellgate London arrived on Friday, and I spent some time (too much time) on Saturday playing it while he was studying.

It is a well crafted game (as one would expect from the crew that did Diablo), but there didn't seem to be enough compelling differences to pull me away from WoW. Granted, the solo play is nice, and I'm only level 10 or so, but I do think I have the flavor of the game.

Uldaman run

2007-11-02T06:48:00.000-05:00

Last night, we did a guild Uldaman run. It went pretty quick, as we had Fingerz (70 rogue) helping out. It is amazing how much damage a rogue can put out. We also had Wrizel, Scrooge, Pinksnappa, and Koen. Wrizel and Scrooge completed 8 quests in there (plus the subsequent chain turn-ins) and gained almost a full level (44.9 to 45.9).

Other than that, I've been working and going to class. This weekend will be a lot of studying, and my daughter has three basketball games, so projects will continue to slide.

Too much WoW?

2007-10-30T06:31:00.001-05:00

Well, Sunday I played WoW most of the day. That's probably too much, but it was a lot of fun.

I also watched the Vikings lose yet another game. The coaches still seem to think that Bollinger is the third string QB, but he's the only one that looked good to me (but what do I know). He had the quickest release of any of the three...but perhaps that had more to do with the play calling than the QB. If so, why don't they call those types of plays more often?

Yesterday was a busy day at work. A new engineer started in my group, and I had three emergencies to deal with, so I wasn't able to spend nearly enough time with him. Compounding things, his access to source control hadn't been set up yet, so he had to copy the source tree off my box. (How can it take over a week to add a user to a group?)

I tried to study last night, but my heart just wasn't in it. I've got to get some studying done tonight.

One of the things that distracted me last night was Tivo Desktop Plus. I purchased it so I could watch one of the Noesis Quickstart videos on a larger screen from a comfy chair, but the Tivo server crashes every time I try to play the video. I hope it's just that video; I'll play around with a couple of other videos, and if they work, I'll try converting the "bad" video to another format or something.

Busy day!

2007-10-27T21:38:00.001-05:00

My daughter had three basketball games today - 9am, noon, and 4pm. All that made it a bit hard to get much of anything done.

We did play some Wii - EA Playground is a lot of fun. All of us are enjoying it.

I haven't worked on any of my projects, nor have I studied in a couple of days - I've just been too busy. At least it's not because I've been playing WoW...

Double Birthday

2007-10-26T00:16:00.000-05:00

Today is my wife and son's birthday. My wife surprised me, and asked for a couple of Wii games; I obliged and picked up Carnival Games, EA Playground, and pre-ordered Wii Olympics. Carnival games is okay; we haven't tried Playground yet.

My son wanted Hellgate London, so I pre-ordered that for him. He also received a Daft Punk CD.

After I got back from class, we had cake, opened presents, and then watched Survivor. Exciting, no? :) We're going to go out to eat tomorrow night (I did't get out of class early enough to go tonight.)

After the party, I played a little WoW. Brizel and I (Neomage) wound up running Ramparts with few other Ice Fury members - Nonnya, Neesa, and Kasch. It was a good group - it went pretty quick and easy.

Humdrum day

2007-10-23T22:41:00.000-05:00

Ok, so nothing all that exciting happened today.

I got up, went to work, went to class, shopped for my son's birthday gift, came home, watched House (good episode), hit Amazon to actually buy my son's birthday gift, and now I'm writing this.

Oh, and my Civ 4 turn just came in via e-mail, so I need to go do that before I hit the hay...

Still on the XSI learning curve

2007-10-22T22:59:00.001-05:00

Well, I've managed to draw shapes and munge them with SoftImage|XSI, but shaders and materials are a whole new ballgame. There is a LOT to learn to even make a simple scene look halfway decent...and I'm not anywhere near being able to do that. I did find a nice little tutorial that talks about glass...but it starts with a scene to download that didn't quite work. I've started reading the materials chapter in the 328-page XSI basics PDF, but it's going to take a while to slog through it.

I'd like to get a scene (er, simple cube) to render somewhat correctly and then ship it over to XNA and see what changes.

Much of the evening was taken up by shopping and studying. I finally went and bought a new pair of sneakers, and found some hiking boots that were on sale (and even my size!) that will come in handy when it starts snowing. (I love my Sorrel's, but wearing them to work/school isn't all that comfortable.)

The usual suspects (Fishlips, Gortel, Spotano, and Dagann) took on some quests in The Wetlands yesterday...we each gained about a level and a half. That was fun, but the day was dreary outside, and the Vikes looked awful in the game against Dallas.

SOFTIMAGE|XSI Mod Tool

2007-10-21T08:57:00.000-05:00

Yesterday I downloaded the SOFTIMAGE|XSI Mod Tool, which can be used to create models for XNA. They have a bunch of tutorial videos on their web site that make it look really easy to create models, but it didn't seem quite so easy when I started playing with it.

I'm not saying its not a great tool; I'm just saying it has a pretty steep learning curve.

Anyway, I want to use it to create the bounding cube and the balls for the first XNA spike. It may take a bit to get the hang of it.

XNA Spike

2007-10-19T23:22:00.000-05:00

I started experimenting with XNA a bit after reading through a bunch of tutorials and docs.

You can check out the (skimpy) project notes on the SourceForge Wiki, or even peek at the source code in the SourceForge repository.

Right now, there is just a bluish box on a black background, and the arrow keys allow the camera to move...kinda. The camera controls don't work right, and I'm not sure why (yet).

XNA looks too cool

2007-10-17T22:00:00.000-05:00

I spend most of the evening looking at XNA in a bit more depth. It seems like the way I should proceed for any rendering that I need to do.

It is a complex topic, though, so there will be a learning curve. I'm going to be spending some time working through some tutorials and futzing around before I can get back on track with my first bio simulation.

The XNA team blog seems to have lots of useful pointers. They refer a lot to a site called creators club online, which (at first blush at least), seems to have tons of content.

I may even break down and buy an xbox 360 controller, as it sounds like they can be hooked up to a PC...

Nova - Ghost in Your Genes

2007-10-17T16:14:00.000-05:00

This morning, I watched a new episode of Nova, called Ghost in Your Genes.

It was fascinating. The focus was on epigenetics, which causes some interesting effects, such as increased rate of diabetes in grandchildren of individuals exposed to feast/famine early in their lives.

It was well worth watching.

3D Graphics in C#

2007-10-16T07:23:00.000-05:00

I spent some time this morning looking at options for drawing 3D graphics from C# code.

I've used OpenGL in the past, so I started by looking for C# libraries to do OpenGL. I didn't see a lot, and came across this post:

You can use DirectX for 3D.
Looking for OpenGL support in .NET is like looking for DirectX support on a Mac.

That made me think I was barking up the wrong tree, so I started looking for some DirectX samples, and came across the Free C# DirectX Control by Jeremy Spiller and a Direct3D Control by Ryan Cook, both of which I'll take a peek at. There is also XNA from Microsoft, but it is not clear to me how much that is applicable to non-games.

And, of course, I could always do the transforms and drawing myself using System.Drawing, but that doesn't seem like a good use of my time.

WoW! Cell Phones!

2007-10-15T21:24:00.001-05:00

Yesterday, I played a little WoW with the gang. My shaman, Fishlips, hit level 25. (I wonder if that makes the VC quests worthless?) We almost had a full group - Fishlips, Yero (my son), Gortel, and Dagann (whose name I kept mispronouncing). Spotano finally showed up two hours late. We finished up all the Red Ridge quests and moved on to the Wetlands.

Tonight we broke down and got cell phones for the kids. It ain't cheap, but a family plan helps a bit. We'll see if they stay within their minutes and text messages (we got the cheapest plan we could).

My Cell Bio professor sent us a link to a cool video: "Cellular Visions: The Inner Life of a Cell". He didn't like the music, but I thought it fit pretty well. It was interesting watching it, trying to pick out all the things we've talked about in class.

Long term goals and a first project

2007-10-14T21:27:00.000-05:00

To quote the abstract of a paper by David Harel:

Biological systems can be modeled beneficially as reactive systems, using languages and tools developed for the construction of man-made systems. Our long-term aim is to model a full multi-cellular animal as a reactive system —- specifically, the C. elegans nematode worm, which is complex, but very well-defined in terms of anatomy and genetics. The challenge is to construct a full, true-to-all-known-facts, 4-dimensional, fully animated model of the development and behavior of this worm (or of a comparable multi-cellular animal), which is easily extendable as new biological facts are discovered.

I share this goal (although I may or may not constrain myself to C. elegans).

To start, I'm curious about embryogenesis and how a single egg cell can develop into an adult worm. I've found a paper entitled "Computer simulation of the cellular arrangement using physical model in early cleavage of the nematode Caenorhabditis elegans" that contains a simple model that I'd like to try and replicate.

One of the initial stumbling blocks is how to render the model for visualization. I've started looking at Direct3D, as well as a couple of C# graphics engines, including Axiom. I'm not sure yet where the project will lead, but wherever it takes me, it should be an interesting journey.

I'm going to give the project the highly creative name elegans2007a.

Once I have this relatively simple model working, I'll begin extending it (or throw it out an create a better model).

School, WoW, Work, Movie

2007-10-13T09:58:00.000-05:00

On Thursday evening, I played WoW for a bit. Wrizel and Scrooge (me) quested for a bit in Stranglethorn Vale, and Scrooge hit level 44. I'm trying to limit my WoW playing a bit so I have time for another things, such as school.

My MyTagMarks project is almost usable - it just needs a few more tweaks to the point where I'll be able to use it at home and work. I spent some time on it yesterday adding the proper formatting for embedded tags.

Last night, the family watched Sweet November, a movie we've seen before (but didn't realize it when we added it to the NetFlix queue). As usual for a Friday night movie, #1 daughter fell asleep partway through.

Today, my daughter has a couple of basketball games, and I hope to get some studying and research done.

Welcome!

2007-10-11T07:08:00.001-05:00

Welcome to the first post of my new blog.

This is a personal blog. My interests are in developmental biology simulation (hence the name of the blog), computational biology, systems biology, c#, .Net, and World of Warcraft, to name a few. All those topics and more are fair game.

My goal is to post here at least once a day on average, even though that may mean some of the posts are a bit mundane. I'm afraid, though, that if I don't stay in the habit of posting, I won't keep going.