A Blonde on Bioinformatics and Aromatherapy

Free SSL Certificates

Quickie: Today only, fressl.com is offering free SSL certificates for a year.

Back to hosting. I found a company I'm pleased with so far. Thanks to folks who responded with companies. I've chosen HostEBiz because they have a feature package that suits my needs and a killer price. So far, tech support has been quick and helpful, the server is fast, and everything advertised is available.

I'm rebuilding the slow shop at Scentgarden into osCommerce. I'm very impressed with osCommerce so far. Maybe there IS something to this open source stuff after all. ;-) You can preview the shop if you'd like, although it's still pretty rough. I've added tweaks to the codebase to hide prices that are zero before the customer selects the size. Next, I need to add radio buttons instead of drop-downs for product options, and hack the categories box so that it looks better. I'm cruising the net looking for an implementation of the tabs on top.

If you see a behavior you like in the shop, just let me know and I'll email you the patch.

To cif or not to cif

To cif or not to cif, that is the question...

I spent a disheartening afternoon staring at some of the new extensions of mmCif. mmCif is the data dictionary for the RSCB protein databank. http://www.rcsb.org/pdb/ It was designed by and for Xray crystallographers. Unfortunately, other people are trying to use the data in ways that were unforseen by the committee that designed the data dictionary.

Bad database design seems to be a hallmark of bioinformatics projects. Most biologists don't understand the importance of a good data model, or how to anticipate how the data might be mined or used. People who know how to model data don't have the domain expertise to understand what they're modelling. So, dictionaries like mmCif become entrenched. They're great for the handful of domain experts who want to capture every aspect of their experiments, but painfully hard to use in any sort of development project.

Well, enought ranting. The moral of the story is, if you're a biologist, get to know a databaser before you do your next project. If you're a databaser, talk to a biologist one day - they might just need your help.

Hosting?

I can't believe how difficult it is to find a good web hosting service. I've been surfing all day now and it's impossible to tell what's what. Does the service actually maintain their machines, or are they reselling? Does the picture of the snazzy datacenter have anything to do with where the computers actually are? Do the UNIX sysops really have a clue? How much should hosting really cost, anyway?

Boy do I wish I had a static IP address. Ah, well. Such is life in the internet lane. If anyone knows of a good hosting service that has PHP/mySQL, supports 4 domains, and is actually reliable, let me know, willya?

Helichrysum

I've found it...the ideal sports essential oil. There's an oil called helichrysum that's amazing for bruising and pain. I got whacked pretty hard in karate class (again) and this time I went home and put 10% helichrysum in jojoba oil on it. The pain stopped within about 5 minutes and I barely bruised. Even better, it's on sale at Scentgarden.

I'll be ready to be a human punching bag again much faster this way.

Caffeine might cause stress

I'm back...didja miss me? Probably not but I'll forgive you this once. Just saw a pretty interesting article on caffeine - every programmer's friend. It says that caffeine increases blood pressure, heart rate, adrenaline, and stress. Now you know why the amped geek in the cube next to you is so stressed out.

Unfortunately, the cure is worse than the disease. Quit drinking caffeine. Yeah, right. Everyone's gotta have one vice, and caffeine is mine.

Karate - what was I thinking

Oof, ouch, pain. I went to Karate class tonight for my weekly round of intense exercise and creative torture. I had to hold a target for a kicking exercise and my partner had a bone-jarring side kick. I'm headed to the bath for a soak in epsom salts, juniper berry essential oil, and rosemary essential oil. It should help - wish me luck.

Clinical trial software will not speed drug discovery

An Rx for the Pharmaceuticals." Getting drugs to market is a costly process without the guarantee of success. Now a cottage industry is springing up to help the big boys save a little dough and pass FDA muster." By Kristen Philipkoski. [Wired News]

Oh, my. This is an article on Pharsight, a software product that is designed to optimize clinical trials. The idea is to speed drug discovery by optimizing clinical trials The product appears to be a biostatistician in a box. Now, the authors of this article suggest that rational drug design and other modeling tools have sped up early drug discovery. I disagree. There were many more new drugs brought to market before the advent of sophisticated computer tools then there are now. Pharsight may be useful, but its impact on drug discovery will probably be minimal because most companies have statisticians on staff with a level of experience and sophistication than cannot be matched by a piece of software.

in the discovery process clinical trial design is not rate limiting. The real problem with drug discovery is the FDA and consumer expectations, not lack of tools. In today's climate, aspirin and penicillin would not have been approved as drugs. Aspirin has many side effects and penicillin can lead to life-threatening allergic reactions. Today's consumer wants a "magic bullet" - a drug that has no side-effects, no risk, can be taken once a day as a pill, and will completely cure their disease in a matter of days. Promising compounds are constantly being removed from consideration because of potential side effects in animal trials. Drugs that must be delivered by injection or taken more than twice a day are also deprioritized.

Pharsight will not change consumer expectations or the over-protective FDA. It might help drug companies save money, but it will not bring drugs to market any faster.