I watch quite a bit of TV and that often includes special episodes or series based on science. Quite often when I get flustered with my own research, these shows will renew my passion and interest for science and remind me of why I am working on a PhD.
I get many of the shows I miss through the internet via multiple methods including web feeds (YouTube), download sites (bit torrent) , and live streaming (p2ptv). Disclaimer: Some of these methods may be illegal based on your location or the tv show provider so check out your laws first. :)
The first show I want to highlight is Stephen Hawking: Master of the Universe. This was a nicely balanced hour long segment that included just enough science along with a history of Hawking's debilitating illness. I remember my uncle giving me Hawking's book, "A Brief History of Time" when I was very young ( I am guessing around ~12 years old). I think I may dig it out and reread it with my much more educated brain.
Thursday, March 20, 2008
Science and Beer
As always, I am looking for ways to improve my publishing and would consider pretty much trying anything. As pointed out in a recent NYTimes article a study showed that drinking less beer correlates with improved publishing.
Personally, I would suggest that the amount of beer consumed is a measure of the scientist's social life and as I think most agree better science often requires less social life. Sadly, I guess I will have to try to be the exception to the rule, since I am not quite ready to part with my bottle of suds.
Personally, I would suggest that the amount of beer consumed is a measure of the scientist's social life and as I think most agree better science often requires less social life. Sadly, I guess I will have to try to be the exception to the rule, since I am not quite ready to part with my bottle of suds.
Monday, February 18, 2008
TrueCrypt
I have never been one to worry about security issues online. I don't clear my cache after online banking, change my passwords every few months, worry about too much information being on Facebook, or even password protect my computers.
However, I have been doing my taxes online for the past three years and I save all of my information to pdfs and text files. I called recently to change my address with the CRA (Canada Revenue Agency) and they ask a ton of verification questions before you can get them to access any of your information. At first I thought this was robust, but then I realized that every single answer could be found in my one folder "Taxes".
After a few quick Googles I found TrueCrypt. It allows you to encrypt a single file (that acts as a container) or a complete partition. If you wanted to go over the top you can even encrypt your whole OS. The default encryption protocols are the same ones used by the top US government (and I assume they know what they are doing). It even allows you to create completely hidden volumes (not that I need that).
I quickly set up a 1GB container to put all of my tax information along with a few other files that contain my passwords that I can never remember . Now, if only I would get around to setting up a good backup system.
However, I have been doing my taxes online for the past three years and I save all of my information to pdfs and text files. I called recently to change my address with the CRA (Canada Revenue Agency) and they ask a ton of verification questions before you can get them to access any of your information. At first I thought this was robust, but then I realized that every single answer could be found in my one folder "Taxes".
After a few quick Googles I found TrueCrypt. It allows you to encrypt a single file (that acts as a container) or a complete partition. If you wanted to go over the top you can even encrypt your whole OS. The default encryption protocols are the same ones used by the top US government (and I assume they know what they are doing). It even allows you to create completely hidden volumes (not that I need that).
I quickly set up a 1GB container to put all of my tax information along with a few other files that contain my passwords that I can never remember . Now, if only I would get around to setting up a good backup system.
Monday, January 21, 2008
Researcher ID
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.
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.
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?
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