Wednesday, November 14, 2007

Fecal Transplant

I couldn't pass up blogging about this recent news article that discusses how transplanting feces to patients with C. difficile can cure their illness. I think it is a great example of how important and natural a balanced microfauna is to human health. I think in a short time we will start to see "probiotic" (I really hate that word) medical treatments on the rise.

Wednesday, October 3, 2007

Least Publishable Unit (LPU)

I have been recently thinking about the Least Publishable Unit (LPU) theory in academia. Considering that I am now a month into my fourth year of my PhD and I have just submitted my first, first author research paper on my thesis work I am starting to panic slightly. I do have a previous first author research paper from undergrad research, 3 other non-first author papers, a submitted first author book chapter, and a Nature Microbial Reviews paper soon to be submitted. However, I would like to have another couple of first author papers in the next year and a half, so that I can graduate with a decent PhD career under my belt.

From my previous experience, the life sciences tend to publish more content less often, whereas computer scientists tend to publish very often with smaller amounts of research. Bioinformatics has overlap in both of these fields thus allowing different publishing rates depending on your research topic. For instance, if you are developing new tools, you would probably be publishing at a greater rate then if you are using bioinformatics to find some new biological interesting result (although this is certainly not always the case).

I would like to think that I have been focusing more on biology and thus my publishing has been slightly behind. However, I now have the skills and knowledge that I could quickly crank out a couple of useful tools that would probably be publishable (I feel like this would be somehow selling out, but maybe not).
Also, if I did go this route does it depend on how much effort was involved or rather how useful the tool would really be?

Recently, I wrote a script that would use gene synteny to make improved ortholog detection in two genomes. It is not overly complicated and uses previously developed tools (genome alignment and local alignment tools), but I think it is incredibly useful and improves upon the basic reciprocal best blast hit approach that is primarily in use. Although, my research is not focused on ortholog prediction and the tool was made so that I would not have to manually annotate 5500 bacteria genes (as part of a bacteria genome project); I have to wonder, "is it publishable?". I guess the only way to find out is by submission.

Tuesday, September 18, 2007

Hogue Strikes Back

Just when I thought the BIND debate was finished Chris Hogue responds to a previous attack with "The other side of staying out of BIND" published recently in Nature Biotechnology.

Personally, I think both sides have a point. Busa's being that we can't fund multi million projects without reasonable returns, and Hogue's that long term funding of databases, such as BIND, is needed.

No matter what side of the debate you fall on you have to appreciate the academic mud slinging from both parties.

Is this my equivalent of reading tabloids about OJ or Paris?

Monday, September 10, 2007

Odd Ball Science

My summer was a busy one that included traveling to Germany, Austria, and England (not bad for my first trip to Europe), plus a trip home to New Brunswick/Nova Scotia. My blog took the greatest hit as I tried to keep up with my research and manuscript writing, but I hope to get back to regular blogging again.

I was one of the thousands at ISMB 2007 in Vienna, Austria and I was presenting a poster on research that I hope to submit to Bioinformatics in the next week or so. Basically, I study genomic islands (large regions of horizontal gene transfer) in bacteria including their identification, their evolutionary origins and their relationship with virulence.

During one of the poster sessions I entered a nice discussion with someone about my research. After about 30 minutes of explaining my methods, background details, future plans, etc. I asked the standard question, "What do you study and is it related to my research in anyway?" and his chipper response was "Oh, no I don't study anything like this. I just like going around to these posters on oddball topics." Now I can take suggestions, criticism, or even indifference, but "odd ball" made it feel like my research was irrelevant; leaving me to puzzle his comment for the next couple of days.

Anyway, after a visit with the bacterial annotation group at Sanger Centre, where people knew what genomic islands were and actually took some interest in my research I was worrying much less about my "odd ball " research.

Monday, July 16, 2007

Open Source Conferences

Last Thursday I found out via Jonathan Eisen's blog that there was a live stream of the Metagenomics 2007 conference. I tuned in over the next couple of days and got a chance to listen to some great presentations. Although, I didn't have any questions I had a couple of offers from people I knew attending that were willing to ask for me. How cool is that?!

I hope that more conferences start webcasting proceedings and/or making the recorded presentations freely available on the internet.

Regardless, there are a few things that are necessary to make a good webcast:
1) All presenters AND questioners must use microphones (this is a good idea regardless of webcasting)
2) High resolution video so that details of the presentation slides can be seen (this is usually a major problem)
3) A nice cross platform streaming media (no windows streaming media)
4) Good encoding so that the majority of internet users have enough bandwidth

Tuesday, June 5, 2007

How do you find science papers to read?

I use a variety of methods to keep me updated on new papers that may be of interest to me, but I am always on the look out for a new tool or method that makes this job easier. Currently, I use the following methods (in order of relevance):
  1. TOC email alert of certain journals (Nature, PLOS, EMBO, etc)
  2. Pubcrawler
  3. myNCBI updates
  4. Papers mentioned in blogs
  5. RSS feed of Connotea groups or similar users
Of course I still have to filter through tons of papers to find ones that I want to read and I often end up missing papers that are not caught by any of these methods. Ideally, it would be great if I had a tool that recorded what I read, and figured out what new articles I would probably be interested in (giving more weight to recently read papers). I think the information from the papers I have bookmarked and tagged in Connotea would be a great starting place for such a tool.

I wonder if anyone else has some tips or tricks that help them filter through the journal haystack?

Thursday, May 31, 2007

Google Street View

Every once in awhile I see a new computer application that makes me sit back and think "Wow!" (and no this isn't an advertisement for Vista). Google added a new feature to their Google Maps project called Street View. Basically, this lets you view panorama pictures at street level of any place in certain cities; currently restricted to San Francisco, Las Vegas, Denver, Miami, and New York.
The cool thing is that you can actually "walk" along the street, look around 360 degrees, and zoom in/out. I'm not sure how the privacy issues will work out for Google since you can clearly view people and license plates, but I can't wait until they expand to other cities (and countries).
Also, Google put out a nice (but kind of quirky) tutorial on YouTube.

Monday, May 28, 2007

Creation Museum

Today is the grand opening for the Creation Museum located just outside Cincinnati, Kentucky. I read about it in a Globe and Mail news article and couldn't help myself from blogging about it.

I am still shocked whenever I hear the statistic that ~45% of Americans believe in Creationism. However, I really wonder if it is fully explained to the people being polled that this means that our planet is ~6000 years old, humans co-existed with dinosaurs, and that millions of species have gone extinct in that amount of time. Have all of these people really took the time to think about what their beliefs are and what science implications are rejected by them by their choice? If so, I would feel much better about the situation.

However, I do worry about the gap between the public and science increasing over time. How do we keep the general public up to date with technology and science when the speed that they are increasing at is so rapid? Does anyone else see this as a potential problem?

Thursday, May 17, 2007

Climate Change Myths

The recent surge of climate change in the media has not really interested me. Basically, I am a bit skeptical that the political interest will last long enough to really make the necessary changes, but deep down I do have some hope.

One of the big problems is getting the information to the public. I think there is a need for information between the high level one page news reports that don't provide any real science and the detailed scientific studies that most people can't and/or don't want to read.

Second, there is usually so much bias in reviews from both sides of the debate that the major facts get missed by the public. Instead, people are inundated with threats of massive storms and flooding or threats of economy collapse. Some people don't want the two major oppositions they just want some basic facts. I think this is similar to the Evolution vs Creationism debate and is one of the best points coming out of Francis Collins' book the Language of God.

A nice example of balancing the level of science and the point of views was published yesterday in the New Scientist. The article provides a "round-up of the 26 most common climate myths and misconceptions" and does so with a true effort in maintaining scientific clarity and an unbiased opinion.

Tuesday, May 15, 2007

Bioinformatics for biologists

I just read the review "Bioinformatics Software for Biologists in the Genomics Era" by Kumar and Dudley. Basically, the authors outline the need for improved bioinformatics software that can be easily used by biologists. I completely agree with the authors, but by the time I was done reading the article I was somewhat annoyed. I think the overall problem I have is that they just keep reiterating that the people developing the tools need to make them more user friendly, without giving any real review of possible solutions or roadblocks that need to be overcome.
They state that:
  1. command-line programs are bad, GUI's are good
  2. being able to submit batch processes is good
  3. documentation is good
  4. clear, human readable results is good
  5. tools that run on all operating systems is good
  6. being able to connect multiple tools in a pipeline (with no programming required) is good

I think even the most amateur programmer is aware of these issues, so I am left wondering who the audience of the article is meant for? In addition they don't reference any of the current tools that are being developed to improve on the situation. In particular they propose:
"Within the context of the user-friendly software, we favor a solution where the existing implementations of computational methods can be incorporated “as is,” without requiring any significant effort from the developer of the program that is being incorporated. We refer to this approach as “Application Linking,” which is similar to “wrapping” (Spitznagel and Garlan, 2003). The aim of Application Linking is to allow existing user-friendly applications to seamlessly host third-party scripts and applications through its graphical interface, such that the user is abstracted from the intricate nuances of the hosted application’s non-visual execution requirements (e.g., process control, system I/O, and control files)."
Ummm.... I guess they haven't heard of Taverna and web services?

As a student who is writing one of these programs let me elaborate on what I think is the main problem. Scientific credit is based on publishing not on producing good tools. What does this mean to me as a PhD student? It means that the time spent on producing a robust web tool would be better spent on making additional tools or conducting more biological relevant based analyzes that will lead to more publishable papers. Am I proud of this? No. Especially since I have a strong interest in reducing programming redundancy, but for now it seems that I don't have much of a choice.

Thursday, May 10, 2007

Directed Evolution

Five days ago I was browsing one of my RSS feeds in Thunderbird that keeps me updated on what other students in the Bioinformatics Training Program are reading and bookmarking in Connotea. Usually, this is for academic purposes, but I came across a link by Ben Good about "What if the Singularity does NOT happen?"**. I took a quick glance at the article and was enticed immediately. I remember a colleague at work mentioning to me something about this book he was reading about the future of human development and technology. I messaged him on MSN and got the name of the book, "The Singularity Is Near" by Ray Kurzeil. I reserved the next copy available at my local library and two days later I am reading about a subject that I knew nothing about a week before.

Now, I should probably hold any reviews or opinions about the book until I am finished, but something in the first chapter bothered me. Kurzweil outlines in one section "The Six Epochs",
  1. Physics and Chemistry
  2. Biology
  3. Brains
  4. Technology
  5. Merger of Technology
  6. The Universe Wakes Up
and explains that,
"Evolution works through indirection: it creates a capability and then uses that capability to evolve the next stage."
This from the surface seems like a reasonable and interesting model, but implies that evolution has a direction. This may work for the last 3 epochs (based on technology), but has the evolution of intelligence (brains) really been inevitable?

Initially, I flat out decided "No", based on the fact that if we started another "Earth" there is no guarantee that intelligent life would evolve. This is due to the fact that evolution works by random occurrences that are selected for by the environment. However, after some more pondering (on my daily 1 hour bus commute), I thought that Kurzweil's theory may have some merit. Essentially, it is the idea that given enough time (approaching infinity) that the probability of intelligent life eventually evolving will reach 1. So instead of directed evolution, maybe we can say inevitable evolution?

I am still not entirely comfortable with this idea, but if I had wanted to increase my personal assurances I would have read a textbook!

**The singularity is an event in the near future where computers will become more intelligent then humans and will result in a drastic change in our society.

Monday, May 7, 2007

Retracting papers

A correspondence article in EMBO Reports discusses how many scientific papers should be retracted. Not surprisingly it found that high impact journals had significantly more retractions compared to low-impact journals. However, they conclude that this is due to the increased readership of the high impact journals and not on the overall quality of the papers.

Open access and internet technology get a pat on the back by the authors when they summarize,
"...the positive relationship between visibility of research and post-publication scrutiny suggests that the technical and sociological progress in information dissemination—the internet, omnipresent electronic publishing and the open access initiative—inadvertently improves the self-correction of science by making scientific publications more visible and accessible".

Indeed, as I am getting ready to submit my first, first author paper, my greatest concern is not that someone will disagree with my findings, but rather that no one will.

Friday, May 4, 2007

Canadian Bioinformatics Workshop

Hello Blogosphere! I told myself about a month ago that I would stop lurking around everyone else's blog and start contributing once I had a free afternoon. Well I am finally here!

A couple of days ago I was asked to be a TA for the upcoming Canadian Bioinformatics Workshop and I graciously accepted. I am really excited to get a chance to do some teaching. I have been lucky enough to obtain funding for all of my graduate career thus far, so I haven't been required to TA any courses before. It looks as if I will be leading a lecture on global genome alignment tools, which is great since I have been using one such tool called Mauve in my personal research (soon to be submitted). Luckily, I don't have to start from scratch since I get to use material from last year's presenter Mike Brudno, who is the creator of the LAGAN alignment tools. Surprisingly, he didn't include any other tools besides his own in his lecture last year. I guess it is natural to talk about what you know best. :)