At least a couple of bloggers have already brought to my attention the press release of ResearcherID. Basically, they are going to allow a user to make a stable and persistent id that can be used to connect aspects of a researcher's profile such as personal web page, CV, publications, etc. This is especially nice for those with a common name that is not easily found using Google.
This interests me since it will allow (I think) a researcher go one step above creating various profiles (ie. usernames and logins) on various sites and enable a single accountable online profile. The only disappointment is that it is limited to "researchers" and not any person that wants to create a unique personal identifier for them self.
I think sites like Facebook, MySpace, and LinkedIn all suggest that all people want a personal profile that they can point to and say "Hey that is me!". However, people are multifaceted and can need various profiles for the different aspects of their lives. Essentially, I would like to have multiple profiles that are all connected to one online person (that is ideally a real person); one for current friends, one for past acquaintances, one for family, one for career relationships, etc. Instead of "adding" each person's Facebook, MySpace, Flickr access to mine I simply add that person (identified by a single id).
Of course this idea is not novel and has been partially attempted before (MSN Passport anyone?), but I haven't found anyone that has done it with enough flexibility and openness to really catch my attention.
Monday, January 21, 2008
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.
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?
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.
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
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):
I wonder if anyone else has some tips or tricks that help them filter through the journal haystack?
- TOC email alert of certain journals (Nature, PLOS, EMBO, etc)
- Pubcrawler
- myNCBI updates
- Papers mentioned in blogs
- RSS feed of Connotea groups or similar users
I wonder if anyone else has some tips or tricks that help them filter through the journal haystack?
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