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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Latest Project: Node.js + Bootstrap + D3

July 3, 2016 at 5:07 pm (Computer Science, JavaScript, NodeJs, Programming, Rant) (, , , , , )

I’ve started putting together an app I’ve been planning for a while. I’ve been trying to select a tech stack that would allow me to focus on the “meat” of my idea instead of spending too much time setting up boilerplate stuff. In the past, I’ve ended up wasting days just setting up technology stacks and libraries just to find a limitation that would eat up even more of my time or even flat-out block further progress. This time around, I think I should be okay; I’ve selected Node.js and Express for my launch point.

I’ve decided not to bother with MEAN.IO right now since I won’t need MongoDB right now and I’ll be using D3 (the visualization library) instead of Angular. Express provides me with the basics for routing and serving web content (more stuff I don’t have to do). I’m still not really a fan of Jade/pug as a template engine, but it’s workable.

I’ve also added an REST API on top of it for accessing my Trello account (via it’s own REST service). I’d like to do some sort of interesting visualization of my content using D3, so now that I can serve up the data I’ll need, I can actually start building the good part.

One of other boilerplate tasks coming up is to set up a client-side package manager (Bower) to manage my dependencies. I will likely also need a task-runner to build my project stuff, although I’d like to consider using NPM for that instead of Gulp/Grunt.

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Story time: Lessons Learned from Contract Work

June 11, 2016 at 3:21 pm (Computer Science, Rant, Thinking) (, , , , )

A while ago, before I started my Masters degree, I tried to find contract work for the summer. I figured I’d need some extra cash when I would move to the east coast to do my Master degree later that year. One of the companies I approached needed a new website; their current one had information crammed in every inch of the view space and it only served up static data. I met with them to figure out exactly what they were after and then set out to build a prototype for them. It was very clear that they knew very little about technology or even what a new web site could do for them.

I took a week to build this prototype for them. It was an ASP.NET web portal with a database back-end, and the whole site was localized as they had a lot of international clients; which I saw as their most important requirement. For the front-end, I scraped most of their base website as their needs were mostly to provide clients with a private access portal, where they could manage their accounts and services. I contacted the company again and set up a meeting to show them what I had made. It had some rough edges (mostly because re-vamping their business-specific pages was a monstrous task that required subject expertise), but it met their needs and was maintainable. More-over, the prototype actually worked; users could sign in, register for services, and communicate using an internal messaging system.

During that second meeting, I received criticism and sarcasm over my prototype. His comments were along the lines of “why would I pay you for a website I already have”. Despite my explanations, he seemed unable to grasp the idea that his $10/month static website hosting was not capable of any of the things his company needed to provide. Because the interface consisted of the same content that he already had, he didn’t understand the amount of new functionality that he would have had with this new piece of software. I was pretty baffled that he couldn’t understand what I had created for him just to GET the contract; not even as a final product.

After several more days of back and forth and modifications to the front-end, I had made a very professional-looking product prototype. I spent effort to make sure it was organized and easy to follow (as far as a mock-up could go), and it still functioned very well for what his needs would be. As it turns out, he loved what it did (finally), but he decided to change his offer: his new offer was on the scale of $10 an hour (citing a bad economy). In addition to creating the whole thing, he also wanted permanent support for it, and he announced that since he was already paying for [static] hosting, he wasn’t going to pay a cent more for it.

At that point I decided I was done with trying to chase this contract. I very politely declined his new offer, and excused myself from his office. I had wasted about two weeks working on this prototype as well as the cost of parking for all of the meetings. I learned a lot of valuable lessons from the whole situation. Firstly, not everybody is capable of understanding vision; some people are just moving objects, not able to see where they’re going. These people need to be dealt with very carefully with “kid gloves” to avoid them from getting in the way of themselves.

Secondly, assertive communication is of paramount importance. If I had forced the questions that I knew needed to be asked, I could have perhaps avoided the whole situation. I wasn’t prepared for others trying to take advantage of me, and I definitely did not ensure we were on the same page. Always be assertive, especially in business.

Lastly, never underestimate the power of idle time. I ended up taking the rest of the summer off to relax and mentally prepare for the stress involved in moving across the country and starting a new endeavor. I finally understand how critical it is to step away from life and take time to clear one’s head.

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Updates: June 10, 2016

June 10, 2016 at 10:55 am (Art, Java, memory palace, Programming, Rant, Thinking) (, , , , , , , , , , , , )

I’ve been working on a number of different things as well as thinking about my next steps and goals for the year. Here is a point-form list of some of the projects and endeavors I’ve been spending effort on in the past couple weeks:

  • I set up a home Linux server. I wanted a local, private Git repository as well as a machine to host some automated processes and apps. Things have been working out very well on this front. It’s been a great learning experience on top of it as well as I haven’t really used Linux in a decade or more. I installed a desktop version of Ubuntu, but I’ve been sticking to using the terminal as much as possible to expand my sphere of knowledge.
  • I’ve been working on my coding skills and algorithm knowledge. I always have some sort of coding project on the go, but recently I’ve been so focused on my front-end skills that I’ve let my core skills droop a bit. To get back up to par, I’ve been solving a lot of coding problems in Java as well as figuring out some algorithms that I haven’t touched in a while. I decided to start basic with heaps and heapsort, then moved on to KMP string matching, and now I am working on suffix tries/trees. I’m going at a slow pace with this though so I can not only code solutions, but also store them in my mind palace.

   Preparing an algorithm for long-term mind palace storage pretty much consists of tearing the algorithm down to its basic elements in your mind and trying to make a story out of it. For example, I’ve decided to store the KMP string matching algorithm in a kitchen in one of my mind-rooms, so I compared the process to making spaghetti. Comparing noodles of different length was the basis of the story. I also had to work in the generation of the prefix table for the search pattern. For this, I’ve been toying around with adding some sort of “sauce” to the story to indicate the comparisons of the prefix to suffix for each length of the pattern noodle.

   I think that I’m finally starting to outgrow the hub room I’ve been using for my computer science mind palace. It was a good index for classes of algorithms so I could always see what tools were at my disposal, but it’s getting too cluttered now.

  • I’ve also been doing a lot of general-purpose reading. I visited the library not long ago and “accidentally” walked away with between 10-15 books. Some of these were painting-related so I could learn some new techniques and composition skills, but I also picked up some interesting biology books. One of these is a book on viruses (the non-computer version). I’ve been learning a lot about how they operate as well as how they’re being used/manipulated today. Bacteriophages are being produced to one day replace antibiotics, and I find the whole thing fascinating (phages are a type of virus that goes after bacteria instead of humans).
  • In addition to practicing my coding/problem solving skills, I’ve also been working on learning and using some new technologies; at least new to me. I’ve been fiddling with the Play framework, which is a web platform. I wasn’t really impressed with it at the start as you have to use a self-hosted web app just to create a project structure, but beyond that it seems really nifty. My next area of interest within this framework is the Ebean integration, which allows for a fun way to connect objects to databases without having to write scripts and stored procedures. There are also some features to allow syncing a database to ElasticSearch automatically, which will be fun.
  • The Android platform is another area I am learning about lately. I’ve set up my development environment and I’ve been learning about the SDK for creating apps. It seems like there are a lot of different approaches to building Android apps, especially as the SDK has been evolving. It has made things a little awkward to get started (as there are many references on the internet to doing things the “old” ways), but I think I’m past that hurdle now. My only real problem now is that I haven’t been spending enough time on this project.

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Progress Update: May 24, 2016

May 24, 2016 at 6:39 pm (Computer Science, Java, Programming, python, Rant) (, , , , , , , )

I know I’ve recently posted about a few of my upcoming goals, but since then I’ve fiddled with a number of things since then and have some updates on my progress.

  • Python Learning. Thanks to a suggestion on the Halihax Slack channel, I picked up a pretty decent IDE for my Python projects (PyCharm). Unfortunately, I learned the hard way that Windows is not the ideal platform for using Python. I wanted to work with a packaged called “sklearn” that I saw during a Google I/O session on machine learning, but it depends on SciPy; a package for scientific calculations. Unfortunately SciPy has some dependencies that do not install cleanly on Windows (LaPack and BLAS are a couple examples). I was really looking forward to toying with the code snippet from the presentation, and I’m sure there are plenty of equivalent libraries I could try out, but the fiddling process wore on me.
  • Android Learning. I’ve been learning about making apps on the Android platform. There was a fair amount of setup and configuration for getting the IDE to work as well as setting up the right emulators to run code on. The annoyances were further compounded by the fact that I don’t want anything installed on my C drive. I use a smaller SSD drive for my C, and then put everything else on another drive; it allows my OS to run lightning fast and lets me get going faster. This guide ended up being really useful in moving the hefty emulators and other odds & ends to my storage drive:

  I’m in a pretty good “hacking” state right now on this front after some effort. I’m learning about the UI-data model binding within Android page components as well as other architecture aspects. The architecture is fairly straightforward (activities, services, etc) but there seem to be a lot of conventions and gotchas.

  • Java Experiments. I’m also back experimenting with Java as well. I’ve been using Derby (JavaDB) as an embedded database, and it’s pretty simple so far. I had toyed with MapDB a bit, but I’d like something a bit better supported so I can use Hibernate with it to avoid having to do my own schemas. I’ve also been using ElasticSearch in parallel. It’s kind of it’s own document-based database, but without the reliability – it’s usually used in conjunction with a real database and you just sync the data in batches so that Elastic can index the data to make it searchable. These components are all pretty straightforward, but I want to build a decent non-trivial demo project. I was also considering using Akka for the concurrency management to control the batch operations to ES.

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Updates: May 2016

May 15, 2016 at 7:03 pm (Computer Science, Java, memory palace, Programming, Rant, Thinking) (, , , , , , , )

It’s been a while since I’ve posted about my recent endeavors outside of painting (this is by design). There’s been a fair amount of things keeping me busy and stressed. That being said, I’ve started putting together and working on my goals for the next several months. A large part of this will be getting my full-stack technical skills back up to a competitive level. I’m going to be focusing mostly on my Java skills as well as commonly-used libraries, since it’s been a while.

As part of this, I spent a bit of time building a small app to back up my development files. Mostly because I needed a good, automated process and didn’t want to go shopping for an app. I needed something that can backup different sets of files at different times, so I could selectively backup specific projects and images, but also my full dev repository. It seems to be working according to my tests, but I’ll be trying it out soon to find out.

I also plan on picking up Python. I think I will use Python 3, although I want to be knowledgeable of the differences from 2 to 3 as well so I can read/port existing code. It shouldn’t take long to pick it up, but I have to learn the specific syntax and rules such as scoping, etc. Some sort of project would help, so I’ll be trying to think of more home automation tasks I could fulfill with Python apps.

Lastly (for this post), I plan on giving my memory palace an upgrade. I need some more rooms, and I need to finish storing algorithms in it. I’m missing tree and graph algorithms (which are pretty important), and I wouldn’t mind adding some more details for implementation as well. This should ensure that I don’t have to review algorithms, data structures, and design patterns when I need to use them; I’ll have them permanently stored.

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My Interview on Dell TechCenter (RE: my inventor status)

April 13, 2016 at 10:39 am (Computer Science, Innovation, Thinking) (, , , , , )

I recently was featured in a Dell TechCenter blog for the innovation work I did last year. I ended up getting a “Top Inventor” title at Dell for 2015 due to my work with filing patents. Unfortunately I can’t really talk about them or even give an idea of how many submissions I made, but I feel like I now have “proof” that I actually did achieve what I said I did, beyond just a LinkedIn title change.

This is the article:


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Convince your Brain to Inspire you with a Memory Palace

September 10, 2015 at 11:22 am (Innovation, Rant, Teaching, Thinking) (, , , , )

If you haven’t heard yet, memory palace techniques are amazing ways to store vast amounts of information in your brain! It has even made its way into popular culture through the BBC show Sherlock and the CBS show Elementary, although the good news is that it’s accessible enough that you can use it without being Sherlock Holmes.

The basic idea of it is that your brain is really great at remembering places; just think about how well you know your own house, your place of work, and the routes to get from one to the other. The trick is that you associate images of things you’d like to remember with difference areas of these locations or routes. The technique is known as the “Method of Loci” and has been used for centuries, although I won’t bore you with the details right now.

I highly encourage you to try out the “Method of Loci” when you get some time, but I’d like to share a specific version of this technique that I make use of every day; I call it the “inspiration room”. You know how some things can get you fired up with ideas? Have you ever walked out of a movie and thought to yourself “wow, that really got me fired up about that concept”? If you have no idea what I’m talking about, I probably sound foolish, but you should probably find more things in this world that interest you.

Anyway, I’ve built up a room in my “memory palace” where I store all of these images that inspire me and make me feel creative. Whenever I need to come up with an original idea or I need to get into a mindset to be creative, I just imagine myself walking around this place and looking at all of the interesting things in this room. It makes sure that I will never forget the things that inspire me and that I can recall them whenever I need to.

Here’s an example of what I’m talking about in case what I’m talking about makes no sense. I begin by thinking about a specific building that I’ve worked in at one point in my life. I’ve spent a lot of time in this building, so I know the hallways and rooms pretty well. I know what the cubicle walls feel like and how sound seems to get absorbed by them. Essentially in my memory I’ve made this place very real by remembering the smells, the sounds, and the feel of things.

So I walk through the hallways of this building, and look in each room; the rooms are where I store my inspiring memories. For example, in one of my rooms I store a scene from the film Iron Man. There is a scene where the main character is building out an upgraded version of his suit of armour that can fly, and he is assisted by his computerized assistant J.A.R.V.I.S. When I first saw this movie, I stayed up until 4am attempting to build my own version of his AI assistant so I could have him organize my life. My memory from that movie and my experiences are something that help me to stay focused and productive. I store Tony Stark in one of the rooms in my mind so I can watch him work productively on his armour.

In case you were curious, I actually did build a basic version of an AI assistant that used natural language processing to activate various tasks. It was fairly successful, but I eventually abandoned the project a couple weeks later. Now it seems that AI assistants are all the rage… whoops…

Hopefully by now I’ve sold you on how useful this idea is. It’s something that I use to stay productive with my time and to get rid of those “blah” feelings when I’m tired. The actual technique of building up this type of room is actually pretty straightforward. First, write down the images that inspire you; you need to know what you’re building before you start. Then pick a location that you know very well. It should be fairly large so you can add new images later on, but it needs to have memorable features such as windows, furniture, or colours.

The last step is probably the hardest one: you have to practice walking through this location in your mind. You have to vividly remember the location and as you walk through it, you need to connect rooms or features with your images by imagining they are there. These instructions may sound a little vague, but your brain actually knows how to do this for you. It just needs to be programmed, and you do this by repeatedly walking through the room and looking at the images.

I hope to tell you about other mental techniques I use on a regular basis in the future. These are really useful for so many aspects of life, and don’t require that much effort to use. Let me know what you think about these or if you have any questions about the technique. I spend a lot of my time practicing these techniques and reading about how others do similar things.

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Dell Innovation Challenge Coin

July 13, 2015 at 3:41 pm (Computer Science, Innovation, Thinking) (, , , , )

So I can finally comment a bit on some of the interesting things I’ve been up to this year. The more interesting thing right now is that I’ve been filing patent applications with Dell. I’ve submitted a number of them so far this year (need at least two hands to count them at this point), and it’s been a blast. I’ve gotten the opportunity to connect with some really smart people along the way, and it’s quickly become the best part of my job. Dell has a great system in place to keep people inventing and being innovative with their work to ultimately serve our customers better.

Last week I received a recognition aware for the patents I’ve been working on; it takes a while to completely get a patent approved and filed, so this award is from the first fiscal quarter. I believe I will be receiving a second (and more impressive) award later in the year for my more recent efforts. Check out these pictures of my award; it’s an innovation challenge coin (similar to what the army does):

Innovation Coin Side A

Innovation Coin Side A

Innovation Coin Side B

Innovation Coin Side B

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Update on Activities: June 8, 2015

June 8, 2015 at 2:58 pm (Computer Science, Programming, Rant, Thinking) (, , , , )

So I had somebody remind me that I haven’t posted anything in a while here. It hit me that it’s been months since I’ve posted an update on what I’ve been up to so I might as well write a few things down. I’ve actually been keeping myself very busy with a number of non-programming projects, so I’ll post a few things.

One of the main things that’s been taking up my time lately is that I’ve been trying to improve my brain. To do this, I’ve been using some software on and off to try and improve my working memory. It’s based on some research called the “dual n-back” test; essentially you’re testes on how many previous numbers you can remember as well as where the numbers were displayed on a 3×3 grid. I believe there has been mixed feedback in the reproducibility of this work as well as its transference to other areas of activity. This means that people aren’t 100% sure that doing well at this test will help you do other things.

In addition to this, I’ve been reading a ton of books from my local library. I believe a week or two ago I hit a point where I had 22 books signed out at one time on a wide variety of subjects. Part of my strategy of being able to read all of these books is that 3-4 of them are books on speed reading. I honestly still can’t believe how much faster it has made me while being able to consciously remember everything I’m reading. I’ve traditionally had attention problems while reading and have gotten used to the lines of text moving around on the page. These techniques have definitely helped me worth this problem.

My last update for today is that I’ve been taking a bigger interest in my career. This has been a theme of the past year as I’ve turned my “normal” job into half of the things I do at work. I’ve been taking on new responsibilities and being more proactive about what I do. For example, this past week I started writing a newsletter for my product’s team to keep them informed on big sales and customer use-cases. This is somewhat of a small thing, but as I keep my ear to the ground at my company for useful information, I saw a need that wasn’t being met by anybody else and opted to fill it.

On a final note, I’ve been keeping better track of all of the interesting things I’ve been doing voluntarily. So I hope to remember to post here more often on what I can (I’m sure there are some things I can’t share for confidentiality reasons).

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