October 2002 Archives

It is finally starting to

It is finally starting to get cooler here in Chicago. Cooler weather always inspires me to get out my knitting needles and start things that I know it will take me years to finish. This year I am trying to be reasonable, however, and focus on small projects I can accomplish or big projects with big wool. I also have a "knitting buddy" this year, and she is also helping to keep me motivated.

I have just discovered bulky yarn and the speed with which it knits up. I got the better part of a sweater knit up over the weekend (the sweater is done with Cleckheaton Gusto 10, which knits up beautifully!) I also just got started on another ladder yarn scarf -- this time using Trendsetter Binario (color 103 -- reds). So far the color is vivid and incredible. I don't think pictures will do it justice, but I will try to take one and post it when I get further along.

Just wanted to make a

Just wanted to make a quick post today to say nice things about the folks at Arcadia Knitting Arcadia Knitting.

My bulky sweater project (Design 11 in the Cleckheaton Gusto 10 leaflet #905) doesn't seem to have the right amount of yarn listed for the contrasting color on the sweater. Not only did they answer my email and set a skein aside for me to pick up when I can, they were also concerned about the pattern's specs. (The sweater is knitting to exactly the gauge and size described in the pattern so I was a little surprised to get midway through the project and realize that there wasn't going to be enough of the contrasting color).

I haven't yet adopted a Chicago knitting store as my "favorite" yet, but after getting a lot of help last Saturday picking out yarns and colors and getting a good intro to Bulky yarns, Arcadia is rapidly moving into that role.

Hmmmm...I guess I should get back to working on my master's thesis project....will write more about it later. Suffice it to say that it is a challenge to convince myself to write code when I have a sweater that I am dying to finish!

You've just got to love

You've just got to love a knitting store open until 8pm! Even I can manage to get there. I retrieved that last skein of bulky yarn that I need for my sweater. Hooray! I also treated myself to a pair of size 13 Brittney needles. Very nice. Inspiration for my next project -- a sweater for my husband.

Unfortunately, no knitting can occur tonight until I finish up some things with my thesis project.

And just what is project that would make me put aside knitting?

Well, last Spring, just when I should have been thinking about which class would be the last one I was going to take before I graduated, I took a class about XML and really got excited about it. You see, there are countless large sources of biological data and almost every source has it's own unique format to parse. Which means that you can spend your life as a bioinformatician just writing parsers.

But XML is nice because you can use the same parsing tools over and over, you just write slightly different scripts to handle grabbing data out of different data sources.

Now, there are two means of doing this. One is based on a DOM (the Document Object Model) the other is based on SAX (Simple API for XML). The long and short of it is that DOM is easy to use from an intuitive sense, but slow and not very good for working with big files. SAX is great for speed and big files, but not very intuitive to use.

At the same time as this happened, I also had come to the conclusion that I wanted to know more about how to design programming languages and compilers. So after talking to a professor who is interested in both, I am working on a project that is meant to take a simple language and convert it into Java code that uses the SAX API to parse XML. This is meant to give you the speed of SAX with the intuitiveness of something like XSLT.

At this point I am just in the early phases of the project. We are still designing the language. Allowing that language to include snips of Java code (so that databases can be talked to and other more complex operations, that are outside the scope of my small language, can be performed) is where I am now. And what I need to finish before I meet with the prof in the morning.

I got all the knitting

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I got all the knitting done on my cropped cardigan bulky sweater project on the way back from my Uncle's wedding in Michigan (Congratulations, Uncle Gary!). I'm now in the process of sewing up the seams so I can work the collar!

Woohoo! I finished my sweater.

Woohoo! I finished my sweater. Now all I need to find is an interesting button. The project worked out well, but the yarn required for the pattern wasn't correct. Will post a picture soon!

I just can't believe that I accomplished something so quickly!

I'm still trying to find

I'm still trying to find a place to store my knitting pictures so that I can display them here. I think we have some space with AT&T Broadband (can there be any better connection than cable, short of having one's own T1 line) but I have to figure out how to use it.

In the mean time, I am trying to add good links to other things that are interesting. Right now I am filling out the "Genomics" section. I'm going to try to add something new every day in hopes of broadening my own knowledge base. Here's what's up right now:

  • Integrated Genomics is the company I work for. We sell an awesome genome analysis suite called ERGO. ERGO is one of my primary responsibilities. Check us out!
  • GOLD is the Genomes Online Database, a database of all the genome projects ongoing that is maintained by a co-worker of mine. He's gotten all sorts of citations for the quality of his site.
  • NCBI is the National Center for Biotechnology Information and is essentially the central US clearinghouse for most things genomic.
  • Ensembl is supported by EBI and the Wellcome Trust (involved in the Human Genome Sequencing Project) and is a great source of information (data and predicitions) for several of the large eukaryotic genome projects (including human and mouse).

I'm moving on to the

I'm moving on to the next phase of my master's thesis project. Converting a SAX-based XML parser interface from a "push" based interface to a "pull" based interface. (Roughly, this means that I have an interface that will give me the next piece of data on demand rather than sending it to me whether or not I want it.).

This is turning out to be neater than I was expecting because it will also likely be multi-threaded. My compiled programs will grab info from a shared memory space and the SAX parser interface will be placing them there. I didn't think my Concurrent Programming class would be so useful so soon. Always nice to be able to put stuff I've learned into practice.

Just added a link to

Just added a link to


EMBL (The European Molecular Biology Laboratory) hosts a collection of very well known and important protein databases, including SWISSPROT. They are also the parent site of ENSEMBL. In addition the also run a BLAST server for the European biological research community.

Just added a link to

Just added a link to

Comprehensive Perl Archive Network (CPAN)

No keyboard biologist's repertoire would be complete without knowing a little about the Perl programming language. CPAN contains Perl source code as well as modules that support Perl functionality.

I have to admit, that while I like the strong typing of a lanaguage like Java, that I can prototype anything much more quickly in Perl.

My husband and I are

My husband and I are off to Ann Arbor, Michigan tonight to take a fall color tour with my parents in Traverse City. I am hoping all the driving will be a good excuse to get some of my knitting projects moving forward. Northern Michigan is just stunning in the fall and we're going to add to the fun by getting on a train to tool around northern Michigan!

I had an excellent trip

I had an excellent trip to Traverse City, Michigan over the weekend. The fall colors were beautiful even though we also got a lot of rain. We capped off the weekend with a trip on the Grand Traverse Dinner Train, which was absolutely wonderful. It turned out to be a very "crafty" weekend for me. I got close to completing a wool scarf project I am working on for my mother. I also am now over half-way through with the Binario scarf. And I started a winter scarf for myself using Berrocco Chinchilla and Glace and a pattern from the Vogue Knitting Scarf book.

While we were driving up to Traverse City I got my mom convinced that she needed to start a knitting project of her own. So we had to search out a knitting store in Traverse City. We found one called "Lost Art Yarn Shop" and mom found the mohair boucle yarn of her dreams (this stuff really is fabulous, in magenta, purple, and blue) and I succumbed to my first Furz purchase. My friend Julie has been saying good things about it for a while, so I thought I would check it out. The one I purchased has a black core with white fur! I can't wait to see how it knits up. I also found button for my cropped jacket. As soon as I sew it on I will have officially completed my first knitting project of the fall!!!

Ugh! The button I bought

Ugh! The button I bought is not quite right. I guess I will just have to wait until this weekend when I can head to Tender Buttons here in Chicago. How disappointing!

I spent the last two

I spent the last two days installing one of my company bioinformatics systems out in the Big Sky country of Montana. The place is beautiful in the extreme.

Over the summer John and

Over the summer John and I got on a weight loss kick, inspired by my father who joined Weight Watchers and trimmed down. John and I are actually close to our own target weights now, too. John's younger brother is getting married in a few weeks, so I promised myself a decent dress for the event, and treated myself to a shopping trip today to celebrate a good installation in Montana and weighing in at 127! I got an unexpected but extremely pleasant surprise when I discovered that I could actually fit -- and fit well -- into size 6 clothing! The highlight of the trip? The lovely stretch velvet, form fitting sleeveless dress I bought for the wedding and an awesome pair of jeans from Guess. I bought some other goodies too, but being able to feel good in the Guess dressing room was one of the highlights of the shopping trip!

I engaged in another theft

I engaged in another theft of ideas from Julie's blog -- the Tag Board on left side and down. You can use it to leave short messages. I should also mention that my friend Julie is an extremely "crafty" person and she runs her own online store for rubber stamping. She is constantly inspiring me to indulge my creative side.

You can check out all the cool things she sells at Stamping Online.

Today was one of those

Today was one of those days when I didn't even get to sit down and take care of outstanding email until 4 pm. We had a big company meeting to discuss how things are going. The future is optimistic, but we are struggling right now. I did enjoy telling everyone about how much fun I had on our trip and how exciting it is going to be working with our new customer.

One thing that I think is true about making the move from academic to "industrial" science is what it means to "do science". Once you are part of a service industry, a lot of people who might hire you just hire you to do a job. You're a contractor, not someone who is meant to be creative for them. I still get a lot of pleasure working on our software, but it is really exhilirating to get to work with a customer who wants to collaborate and give us room to be creative and innovative for them.

I actually got back to

I actually got back to my mission to take a look at more good links related to my fields of interest. That is one of the joys of bioinformatics -- I am a geek in not one, but two fields. Today's links represent both today.

  • Slashdot If you use Linux or other open source software in your day to day life you ought to know about Slashdot. Even if you don't you can check them out to get geek-worthy news and interesting insights into the hacker personality. I look at this site everyday. Sometimes twice.
  • GenomeWeb is one of those websites that most of our scientists go to for bioinformatics industry information.
  • Bioinformatics.org News about bioinformatics and open source sofware, combined. Also lots of links to software tools. Definitely worth checking out.

I moved the TagBoard up a little bit to make it more visible. I'm trying to include the ability to leave comments for particular posts, but until then, if you have something to say, shout it on the Tag Board.

I found out about a

I found out about a neat distributed computing project last night by watching my husband surf his favorite home theatre message board site. It combines both biology and computing and it's a good cause, so I thought today I would throw the link out.

The project is called Screensaver Lifesaver and it is run by Oxford University. The idea is to use unused computer cycles all over the world to screen small molecules for their ability to combat cancer. This project is similar to the SETI at home project. The only downside is that the software only works under Windows.