BioHive: Bioinformatics blast from the past

July 7, 2016 at 10:30 am (Computer Science, Processing, Programming) (, , , , , , , )

Lately, I’ve been combing through some of my old projects so I can index and archive them. Among these old projects was my BioHive code; a bioinformatics visualization tool I wrote years ago. It was an attempt at exploring genome comparison data sets. It was actually the first non-trivial Processing (P5) app I wrote.

Different genomes would get organized into layers (indexed using colour) and nodes would be joined together based on similarity strength. Thickness of the lines would indicate connection strength, and filters could be applied to reduce clutter. Selecting a node in a layer would show information on the genome it represented as well as the top similar genomes.

These are a few screenshots of the app. In this example, Syphilis is the point of interest and they are just different views of filtered results.

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Video: Second demo for my game

April 3, 2015 at 3:38 pm (Game Development, Games, Processing, Programming, Video games) (, , , , )

I’ve finally gotten around to making a video recording of my new game demo! Part of my problem was finding a suitable video capture software suite. I ended up using Open Broadcaster Software, and it turned out fine; I WAS using KRUT, but it had issues with the audio capture.

Anyway, while recording it I ended up finding out that half of my rooms didn’t make it into the demo! I had an issue where a locked door led straight to the boss level. That kind of sucked. Here’s the video though:

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Update Mar 12, 2015: New game demo, mind palaces, and notebooks

March 12, 2015 at 1:29 pm (Game Development, Games, Processing, Thinking) (, , , , , , , , )

It’s been a while again since I’ve posted here, but I haven’t been idle in this period of time. I don’t think I can list all of the things I’ve been up to, but here are three things I’ve been up to:

New Game Demo

I’ve recently released (privately) a new demo for my game. It features brand new levels, mechanics, and storyline. I’ve even added new tilesets and original music for the levels. With the last demo, I was happy to have something playable that resembled a game and showed off some of the neat things I’ve built, but this time I think I’m actually content with it as a game. I’ve added some dialogue that needs a bit of polishing, but is roughly what I want it to be as well. I still need to post screenshots and a video, but I need a big chunk of time to do that still.

The first person to play-test it and give feedback made me pretty happy. It seems that they felt what I wanted them to feel and thought what I wanted them to think with respect to the storyline. They noticed some of the extra details I put into the levels (like the rain effect) as well. One thing I took away though, was that they didn’t use the camera mechanic at all. I think I might add some HUD cues and mechanics to encourage the usage of it.

 Mind Palace

I’ve been spending a considerable amount of time lately rebuilding my “Mind Palace”. This is a mental tool that utilizes the “Method of Loci” method for memorization. Essentially it’s a superior way to reliably remember things. It takes a bit of effort to set up and upkeep, but if done correctly, you can do wonderful things with it.

Before, I was building the hub structure of my palace based on something I had imagined. My problem was that I never fully constructed it; I wasn’t sure how big of a space I needed, so it deteriorated over time faster. I can still reference most of the rooms, but I didn’t solidify where everything was enough.

Also, I didn’t have enough connections to well-known places. Examples of these are houses I’ve previous lived in, These are useful as you can typically just imagine yourself moving through those places and then have your memories jump out at you. My next goal is to tie in more of those to my “hub area” so that I can jump from location to location without having to remember how many houses I’ve lived in. It probably would look like that hallway in one of the Matrix sequels that had all the doors leading to difference places.


Soooo, it turns out I am a crazy person? I used to have decision issues when it would come to notebooks. I remember being in a store for 10 minutes trying to decide what colour I wanted to use for a notebook. I ended up just buying all of them so that I could decide in a non-public place. Recently, Target has gone out of business in Canada due to questionable decision making. The good part of this is that Moleskine notebooks have gone on sale; at the time I purchased them, the discount was 30% off. I rarely notice these going on sale, and since I’ve started using them almost exclusively, it seemed like a great idea! However, now I have a drawer full of different sizes of notebooks and my mind will only let me use certain notebooks for certain purposes. I’m happy to not have to go buy more for a while, but now I have to store a ton of notebooks…


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Zombie Mansion with shaders and post-processing

January 22, 2015 at 9:03 am (Game Development, Graphics, Java, Processing) (, , )

Update: Full project description here

I finally got around to retrofitting my older projects with the new hotness. I am now rendering the scenes with shader programs, which gives me a lot of nice options for how the scenes look. I can do lots of fancy stuff with them including doing neat things to the screen after the scene has been drawn. Here’s a quick example of one of the things I’ve already tried. It’s a ripple effect I applied to the screen; it looked awful, but I was getting 60 frames per second with it (which is good).

jan17_2015_screen effect gone wrong1

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Project: DarkWolf2D (2D Dungeon Crawler)

January 10, 2015 at 4:30 pm (Game Development, Games, Graphics, Java, Processing, Programming, Rant, Uncategorized, Video games) (, , , , , , , , )

Over the holidays, I had some time to upgrade the core code for my game engine. I’ve upgraded the version of Processing that I use as well, which means I can use shaders for rendering along with some of the nicer JSON loading features. While I have a “version 2” of my engine working though, I haven’t yet retro-fitted it into my Zombie Mansion yet. This is coming in the future, but for “proof” that my code works, I’ve been putting together a small game based on a design I had in a dream. It’s the “basic” version of the idea, which means no multiplayer and no nice graphics.

The idea is for a dungeon crawler action game that takes ideas from the MOBA genre. I know how it sounds, but it’s actually a very basic idea and it’s already half built. It’s a player-vs-environment game right now where the player begins at level 1 for each dungeon and has to level up as they progress to bosses. The theme for it is an alternate history WW2 where the characters are different classes such as “US Medic”, “Russian Sniper”, or “French Resistance Fighter”. Each class has a basic attack and a list of abilities they can level up and use. I’m keeping the XP system as simple as I can (although I’ve never built one before), and I’m not using any items for the game right now.

For rendering, it’s a 2D game with no character animations; just a static side-shot image. This should keep the dev cycle pretty low for now. I also have a feature backlog that I’m considering making public, but for now I’ll only do that if I have anyone comment that they actually care to look at it. It’s a list of all the features that I plan on implementing (some are basic things like “add audio to the game”, and it functions as my “todo” list. As I build in features, I mark them as “Complete” and they shuffle to the bottom of the list for storage.

Edit: Added a screenshot. It’s very basic and you can’t really see anything worthwhile. Just showing that I can at least render the player in a level. I’ll make a video later.

First screenshot of DarkWolf2D

First screenshot of DarkWolf2D


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Markov Chains for Procedurally Generated Textures

October 22, 2014 at 5:48 pm (Computer Science, Game Development, Graphics, Processing, Programming) (, , , , , )

As anybody who’s spent time on this blog knows….well, anyway, I’ve spent a while working on my game on and off. One of the time consuming processes of this was to build textures and level details. All of the art from the screenshots was created by hand using classic MS Paint (not the new-fangled one that comes with Windows 7). One particularly tedious aspect was making bookshelf textures. I had to manual rearrange books and come up with different combinations of books that I thought would be “believable” by the player and not repetitive.

Well, here’s where my new project comes in! Last weekend I spent a few hours writing an algorithm that would generate shelves of books for me. Why is this interesting though? Couldn’t I have just randomized the books and called it a day? Well, the problem with strict randomization is that it looks ugly. It would just be a mish-mash of different coloured books, which is fine for a modern bookstore but as my game takes place in the 1920’s-1940’s, it felt more appropriate to have a bit more organization. Essentially, in older libraries you would be more likely to find books that looked similar because of binding techniques of the days. You’d also find more books that were series of something that would have the same style of cover instead of just a colourful, different cover.

The goal for this project was to generate shelves that had clusters of books. To achieve this, I used a Markov Chain algorithm that would place each book on the shelf one at a time. Depending on the book it would place, it would favour specific types of books for the next book. There is still a randomized aspect to the algorithm, but it is more constrained depending on the state.

Below is a screenshot comparing some of the results of the algorithm to a strictly randomized approach. As you can see, both are somewhat random, but the shelf on the left shows more groupings of similar books.

Procedurally generated texture comparison

Procedurally generated texture comparison



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Aftermath of Zombie Mansion Alpha 1 Build

July 18, 2014 at 12:40 pm (Game Development, Games, Graphics, Java, JavaScript, Processing, Programming, Video games) (, , , , , , )

So at this point in time I’ve had multiple people play through my game demo. The results were actually better than I thought. I think only one person wasn’t able to run it (still not entire sure why, but that’s future Jake’s problem now). There were a couple major issues, but those were found and fixed as well. One of the bugs was that I didn’t include the assets for the 3D objects, so when the players entered the room with columns, the game crashed. There was also some scripting errors driven by not having necessary images wrapped up in the resources archive. Logging definitely helped out there.

The last major issue is unsolved, but lies with some code I threw together for the level selection screen. I think some of the click events aren’t going through, or it’s not loading the levels properly. I think this may have something to do with that particular tester running the game through a zip file though. I was shocked to find out that it worked period though.

I got some pretty decent feedback from one tester in particular though. He gave not only bug reports, etc, but opinions on controls, aesthetics, and game flow as well. Most of those things were explained away as “placeholder” stuff, but still; it was useful information to know what a tester/player is thinking when they see that stuff. When I show most people my game, I need comments like “looks neat and retro” or “I like the camera spin feature”, but not enough people pay attention to tiny details.

Anyway, that’s the update. I haven’t had free time to cut a second build or to work on new levels or anything.

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Ant + Processing = Grief

July 4, 2014 at 8:20 am (Computer Science, Game Development, Java, Processing, Programming) (, , , , , , , , )

This will be a humorous post coming right after the article about how great automation is. After I finished writing my Ant scripts for automating my Java project, I ran into a wall; Ant can’t update a Processing library while the Processing Development Environment is running. For some reason, Eclipse is able to deploy JAR files and have them overwrite the existing library while the PDE is running though!

So now I have to figure out a way to make this work, or else I have to ignore all of the automation I put in. I may still use Ant to back up my code projects to an external hard drive, but that’s about it right now.

And then there was sadness.

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Automation 4 U

June 28, 2014 at 2:29 pm (Computer Science, Game Development, Games, Graphics, Java, JavaScript, Processing, Programming, Rant, Teaching) (, , , , , , , )

So, this will be nothing new for some of you. This isn’t even something new to me; I have a day job where I’m a professional software engineer and we do this at my job all the time. I’m talking about automation and automated processes. This could be anything in your project development process where you have the computer automatically do something for you. An example could be a script that backs up your files to a different drive that you can just run when you want. It could be as complex as a build step that automatically deploys your binaries or runs unit tests.

My disclaimer: A lot of this is technical stuff and directed towards programmers, but even if you’re a graph artist, you can still benefit from this. Everybody that uses computers for projects will need to back up their files for instance.

I’ve only recently realized just how important this all is for regular, personal projects. I’ve always known that it saves time, but my initial mindset was that I’d rather get my project up and running and THEN waste time implementing the time-saving stuff after I get it together. I’ve been reading this book I bought from Amazon that talks about indie gaming from a business, “get your act together” perspective. The book can be found here. I’m still reading it, and some may or may not agree that it’s a good book, but it provides some good ideas for how to take your hobby projects to the next level and keep your process renewable. This means saving time and money on mundane processes, etc.

I am still in the process of automating many aspects of my project, but it really crept up on me just how much time I was wasting on manual things. Here are some of the processes I perform just for my Zombie Mansion project:

  • Backing up files from two areas on my system to my external hard drive
  • Deploying JAR files from my Eclipse solution to my Processing solution to use in my game
  • Removing alpha channels from sprite sets (I built a tool to do this, but it’s still manual)
  • Putting together standalone builds of the game software
  • Packing and compressing image resources for game builds
  • Merging animation sequences together for access by the game engine

These are just things I thought of off the top of my head this morning. Some of them will be easier to do than others, and some of them are specific to my project. All of them eat up time though and are tedious things. Here are a few tips and ideas for how I plan on solving some of these issues though. Please read through just in the off chance that it inspires something or gives you an idea or two.

Deploying JAR files to another solution

For this, I intend on using ANT with Eclipse. This is pretty much a standard for serious Java projects, but it’s taken me a long time to start to improve my processes (usually I want to work on the fun stuff or the stuff that has a visual out-come). Visual Studio has its own build steps and things you can run. Alternatively, you could write a script/BAT file that will grab the files from your output directory and deploy them. This doesn’t require a full set-up of a 3rd party tool and it should be quick to do. It just might break and won’t be as robust.

Backing up project files

This is something I’m already part way through implementing. I’ve written most of a BAT script that will grab the project files from specific directories and dump them in one area so I can back them up (it will optionally zip them as well). To make it a bit easier, I’ve started using virtual drives, but this isn’t necessary. If you’re interested in what virtual drives are or how to set them up easily, email me or post a comment. I can give you some resources or just write an article. Here is a snippet of what I have so far (I’ve been taking bits and pieces from the interwebs, so most of it is borrowed code anyway).

I wanted to dump the files into a folder that would be timestamped so I wouldn’t have to worry about overwriting anything. This is one way of how you’d accomplish it using a BAT script in Windows:

set hour=%time:~0,2%
if "%hour:~0,1%" == " " set hour=0%hour:~1,1%
set min=%time:~3,2%
if "%min:~0,1%" == " " set min=0%min:~1,1%
set secs=%time:~6,2%
if "%secs:~0,1%" == " " set secs=0%secs:~1,1%
set year=%date:~-4%
set month=%date:~3,2%
if "%month:~0,1%" == " " set month=0%month:~1,1%
set day=%date:~0,2%
if "%day:~0,1%" == " " set day=0%day:~1,1%
set datetimef=%day%-%month%-%year%_%hour%-%min%
echo %datetimef%
xcopy "C:\Test\A" "C:\Test\B\Backup\%datetimef%" /E /I

This will copy everything in your source directory (the first argument) and store them in a custom folder with a timestamp. You can use multiple source directories as well if you have things spread out like I do by just putting in an extra line. The last two arguments are switches to tell XCOPY to use the full source directory (and children) and to assume I mean the destination should be a folder.

Removing alpha channels from image resources

This one will be a bit more complicated. I have a tool I wrote to do this, but I want to streamline this. Now, I wrote up a full project plan with a product backlog, but then I realized even that was too ambitious. I plan on taking some items from the list, but I also plan on it being a purely script-based tool. It will run on the command prompt and will use my engine’s scripting engine for customization (as opposed to using config files). At this point in time, it’s cheaper for me to use scripts than config files since I don’t have a streamlined approach to reading them yet. ANYWAY, I will be writing this as a project in my game engine solution and it’ll have a unit test project to go with it. I’m still working out what tests I will need for it since it works with images, but it’ll be centered on testing the RGB values of generated images before and after the script runs. It’ll also test image sizes for when I add the feature to compile multiple animation sequences together.

Anyway! To summarize this; automation is good. It saves a HUGE amount of money (time is money). If you ever have dreamed of selling a game, you NEED to get in the habit of doing this. The more you do it, the easier it will become and the more effective you will be with your time. Be as lazy as possible with your projects; that’s why we’re programmers! (Although you don’t need to be a programmer to benefit from this).



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Zombie Mansion: Alpha Build 1!

June 23, 2014 at 2:54 pm (Computer Science, Game Development, Games, Java, JavaScript, Processing, Programming, Rant) (, , , , , , , )

So I’ve finally gotten a build of the game working! I can’t post it yet for a variety of reasons, but I’ve sent the build out to some people to try it. It’s mostly to verify that the game works as expected and is stable. It just features the level I showed in the previous videos and a couple of extra smaller areas.

Last Saturday night I had a few panic moments when the builds weren’t working as expected. I had an issue where the resource unpacker code I wrote wasn’t actually unpacking the images from the compressed assembly; it turns out it was still trying to load them from the local directory. The issue has since been fixed thanks to all of the logging architecture I recently put in. There’s still several areas that could use more logging, but there’s enough now to sort out common issues.

Another bug that logging helped uncover was with the asset manager system. I have code that manages any images and ensures you only load one copy into memory. This helps to keep a cap on the memory usage of the software as a whole. However, there was an issue where I had slashes in the reference indices that were going the wrong way! This is a pretty common issue with programming to be honest. Devs frequently write code for their own system and then find out that nothing works on other computers or operating systems. Thankfully, the logging system helped uncover the fact that it was double loading certain resources.

Now if I could just muster the effort to change the spelling mistake I made with naming the logging variables…

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