This is an archive of my weblog that used to be entitled "The Struggling Grad Student." I decided to keep this blog online since many people are still sending me emails about the tech info and grad school related entries that I wrote. Click on the "Full Archive List" link below for the whole shebang.
Portrait of a serial sequencer: Not even the sky is the limit for genome giant's grand plans. There has been lots of buzz about Craig Venter going around in the blogging world. Richard Gayle posted a little synopsis and commentary on his blog. Snowdeal.org also has a blog entry. I had the opportunity to speak with Dr. Venter when he visited the campus two years ago (or was it 3 years ago?). We talked a little about bioinformatics and the technology he used. I do remember that he commented on his moving terabytes of information on a weekly basis. This was during the heyday of the stock market, and he was worth a few hundred mill on paper at the time, with his stake in Celera. This was also before he made public that one of the sources for his human genome sequencing project was him. Surprise surprise, even the brightest among us can be guilty of some vanity.
Google US Puzzle Championship. Google has a challenge for you, if you want to participate, you must register TODAY! Think you have the brain to match your brawn? Or maybe you are all just brain? If so, finish the sample puzzles on the page, and if you got game, sign up and get the chance to win a trip to the Netherlands for the World Puzzle Championship in October. Grad students represent!
Finally had the chance to listen to some of Anthony Robbins' "Awaken the Giant Within" audio lecture (nice thing about having an MP3 player -- highly recommended for all students or commuters) on my way to work and back yesterday. Really had me thinking about my situation. I'll distill down for you what I've listened to so far.
Essentially, your life is dictated by the choices you make -- hmm, sounds like the Matrix doesn't it? Beyond choices, however, Tony Robbins tells us to think proactively and make decisions, not just choices. The difference? Well, the difference is something I've contrived, but in essence, when you make a decision, you are exercising your "decision-making muscles" as Robbins puts it. It is exactly what you'd imagine -- you are actively deciding on an action, to execute it and learn from the results.
Well, for the first part of his talk, the theme was empowering yourself to make decisions. The second part of the talk had the theme of beliefs and how your beliefs dictate your decision-making. I'll comment on the second part another time -- well, actually, when I finish listening to it. However, the first part of his talk opened up a plethora of observations. The obvious question was "how does this theme pertain to me as a scientist?" The obvious response, then, was "scientists should have the inherent ability to make well-thought out decisions based on past experiences." Well, needless to say, this brought me down to a feeling of utter bottomless despair. Why haven't I been able to make the correct decisions that lead to fruitful results? After all, I am a scientist right?
In an effort to mend my feelings of outright failure, I continued listening to Anthony Robbins further. In one anecdotal account, he describes how one scheduled seminar at Glendale, CA caused a traffic jam in and around the convention center hosting his seminar. He had, as he recounted, about 7000 people attempting to attend a seminar in a hall that could only house 5000 people max. Now, if what he's telling us is true, for that many people wanting to attend his talk, it means that there are at least equally as many people in that area that have felt what I felt -- a total failure. Follow me so far? So it must not be unfathomable to think that there are scientists out there who feel the way I do? So if this is the case, the assumption that scientists should "inherently" be able to make the right decisions is false. Now, debunking this myth means that I had to go on and try to find a fix -- hence, I listened even more intently to Robbins.
The answer as to why I am in this "rut" was suddenly apparent to me. All along, I've been going with the flow, in terms of my science and even my education/learning-process -- trying to gauge what my mentor thought was the next step in the experimental process. I needed to be more proactive in my decision-making regarding the scientific process. In fact, I needed to wrestle total control over what I am doing at work. The more I make decisions and learn from them (on my own), the better and stronger my "decision-making muscles." For me to get out of this "rut," I have to: 1) re-evaluate what is important to me at work, 2) actively decide on a course of action, 3) learn from the consequences that result from these actions, and 4) re-apply what I've learned to my next decision-making moment -- these are the four tenets that Robbins layed out, and quite obvious, these are the four steps that successful scientists essentially take day-in and day-out. Bottom-line: I had to be more PROACTIVE in my decision-making. Enough about me.
The second thought that came to me while listening to Robbins was "man! 7000 is a lot of people. Lots of unsuccessful people who are missing something enough to want to listen to Tony Robbins!" Strangely, I then thought: "would that many people show up if he was in a Third World/developing country?" I then digressed into this thought of how developed countries like the U.S. have a disproportionate number of people who are glutinous -- complacent in their situation, well-fed enough to not really care about anything else. Why, then, should this complacent behaviour be any different in other aspects of life, like "decision-making." Having more complacent people in the population should mean that there are more people who would rather just "go with the flow" and not be proactive in their decision-making process. Hence, because of the disproportionate number of people who are lax in their decision-making here in the U.S., when the "s#@* hits the fan," more of them will be coming to Tony Robbins. Am I wrong in this sequence of associations? What a strange sequence of thoughts. To validate this belief, think about the number of recent immigrants that become successful here in the U.S. For these individuals to come here, it must mean they are highly proactive in their decision-making -- a behaviour that is tough to lose when finally here.
I'll just close here. If you are a graduate student, and my thoughts here reflect your situation, please place a comment about it. However, if you are a student who has found the key to a successful scientific career, I would love for you to comment as well. I really want to know -- are there more grad students like me (feeling like a total failure), or am I the exception to the rule?
Finally was able to see Matrix 2 last night. Very entertaining. Good thing Bruce Almighty came out this week (the line for that movie was crazy) -- meant that less people went to see Matrix 2. In fact, there were plenty of empty seats for Matrix during my viewing. I don't want to spoil it for those of you who haven't seen it, but the themes in this movie that you will encounter (and I will relate some of them to biology) will be:
1) Man needs machine to survive and in the world of the Matrix, the opposite is also true. We all know what symbiosis in biology is -- should have been something we all learned in 3rd grade?
2) "We" all learn from past mistakes -- in the story of the Matrix, "we" includes humans, machine, and computer programs. I guess mutation can in a way be thought of as a process of "learning" -- i.e. improvement. BTW, mutation of computer programs in the Matrix is possible.
3) Love can make you do some crazy s@*# and love is a human emotion that no machine will acquire, that no program can simulate. Or can they?
4) Choice in the Matrix is an illusion -- the age old argument of nature versus nurture. "Did that guy go psycho because it's genetically inherent in him to do so or did his environment cause that in him, or a mix of both?"
5) The them of choice leads to the common theme of cause and effect, action-reaction.
Lastly, I'll close with a question that was hinted in the second movie and will probably be answered in the third installment: if humans can "tap" into the Matrix, can the reverse situation be true, i.e. can programs within the Matrix, come out of the Matrix and learn more about the human environment? What are consequences of such a possibility? How extensive is the reach of a human "tapping" into the Matrix, and vice versa?
That's it for now, got to get this presentation done for this coming Friday. Been dragging my feet to put together the slides.
My blogshares at BlogShares - The Struggling Grad Student has just been listed for trading! Woohoo! I'm being sold at a bargain basement price of 25cents per share. There are currently 4000 shares publicly available -- I could, in theory buy 1501 shares and be the majority stockholder of my blogcompany (I'm given 1000 shares off the bat), but since this is for fun, I'll let it ride in the free market and see how far I can go. So, you want piece of me? Think I'll make you some fake money? Put your money where your mouth is and buy some already!
In other news, been playing around with the b2 blog engine. Nice piece of free software. I've set it up for my cousin's blog, who's finally using it. It has all the pieces that make it interesting to me -- written in PHP with a MySQL backend (although I hear it can also use PostgreSQL), making it highly hackable. You ought to check it out. Alas, I'm not using that blog engine for this site because: 1) learned about it too late and 2) already made a donation to MovableType.org for my blog engine. What I've been hacking on b2 to allow it to use MT CSS files. In theory, then, all that is needed to have MT CSS files interchangeable between a blog using MT and another using b2 are the files that I've hacked. When I feel the hacks are worthy of publishing, I'll put it out here for you to see. In the meantime, check out my cousin's site for an example of a b2 blog.
I thought about writing a sed script to easily convert b2 files to use MT CSS files -- maybe when I have some free time or some monetary incentive to do it.
Want that extra kick to your audio blog? Have a need for a radio commercial and need professional work? Surf on over to a good friend mine: Jeffrey T. Mason or try Voiceovers. Seriously, he does quality work, just check out the demo and his history. He'll help you out. Tell him I sent you.
Been such a close part of my life for nearly 6 years. Always helpful, and I've always felt lost without you. Now that you're gone from my life I don't know what to do...Yep people, my Sprint PCS phone is officially dead. It powers up, but gets no signal anywhere. Need to find a replacement, any recommendations? Wonder if I should just switch carriers completely and go with say, T-Mobile, with a package that includes access to their WiFi Hot-Spots. But I've been with Sprint for so long -- close to 10 years, at a time before they rolled out PCS and had their own Sprint digital network -- that I don't want to dump them, unless of course T-mobile gives me a sweet deal. Then there's AT&T and Verizon carriers to look at. Man, too many options, and too much money to sneeze at.
Got the Monday blues, need to get this sequence out to a collaborator ASAP, but can't seem to get myself motivated -- been thinking about my son's skin problem with atopic dermatitis (AD). I wish there was a treatment for him that was certain-- Elidel and Protopic do not help. I'm so frustrated with this problem. I wish the true cause of AD was known -- how could 10 to 15% of infants suffer from this and a cause not be known? And no agreed uniform treatment? Had blood tests done and he's not allergic to any of the big allergens, like milk protein, pet dander, etc. I have a feeling he'll be suffering from this condition until it diminishes on its own (usually by 18-36 months) -- and we won't figure out what makes him sick.
I was reading my friend's most recent blog entry. Not uncommon to google oneself. But I have to say, I got him beat. Currently I'm number 13 on the US Marshals Most Wanted List. I've actually moved up on the list! Last time I checked, I was at number 14. LOL! I wonder if I could collect the reward on me, if I called the US Marshals. Funny thing is, I was once pulled over by the po-po for no apparent reason. I asked him why I was pulled over and he mumbled something to the effect that he thought I was someone else. How do you explain that? Coincidence?
My ISP was having problems yesterday, apparently. The upgrade must have screwed something up and so it was out from 2pm to 9pm yesterday. Hopefully no more problems from this point on.
Still debating whether to fight the crowds tonight and go see Matrix Reloaded. TGIF.
Finally got around to playing with some old footage on the digital camcorder -- now that I got a Firewire CardBus card for the laptop. The laptop is a little too slow for complete video editing, but good enough for gub'ment work. Here is a little clip that I downloaded last night (my apologies, it's in WMV format, so you'll have to d/l and play or use Internet Exploder):
Microsoft Movie Maker has a minor learning curve, but isn't too bad at first glance, fairly intuitive. I've heard good stuff about Adobe Premiere and iMovie on the Mac -- haven't used either software, so I can't comment on how Movie Maker compares. Major downside with Movie Maker is that video is compressed as a WMV file which is next to impossible to convert to other formats for web publishing (from what I've read) -- but perhaps I'm wrong, can anyone prove me otherwise?
My site will not be accessible tonight from about 11pm to 6am. Just received word from my ISP that they are performing upgrades on their systems, which will lead to the downtime. Not that it's any matter to you anyway, since what, there's about 2 of you out there who read this?
Just got a new PCMCIA adapter for my laptop. We'll see how well it handles video from my dig camcorder. I hope it wasn't a waste of money. Anyone out there have recommendations for free/open source video software that simply downloads the video feed and burns to SVCD on CD-R? I don't want anything that takes a lot of user input -- rather, I'd like something that I can set and forget about until next morning.
Pubmed module is back - nodalpoint.org. These are exciting times. Witness this everyone -- 2003 will be remembered as the year of new beginning in the industry of scientific publishing. Lots of things will happen, mark my words. The link above points to a blog entry by Greg who has also developed a blogging service to comment on papers -- although I don't know if it allows TrackBacking as pmbrowser.info does.
I've been holding back a concept that I think is a workaround/simple hack around the problem of access to papers that Greg has also mentioned in his blog.
I am foregoing possible riches and will reveal it to the public, hopefully for the betterment of the scientific community. In fact, I did submit this to slashdot, but the article was rejected (yet more proof that slashdot does not know good blogs when it hits them straight in the face). The following is the entire submission:
journal prices have been increasing at a breakneck pace. As a graduate
student, my experiences with accessing journal articles has been
horrendous, to say the least. There are too many restrictions and high
costs associated with access and it has been made a noticeable dent in my
productivity, especially at writing time (i.e. writing my own journal
article), a time when I prefer instant access, on my computer, to articles
that I have read or that I need to read. This is not to say that the
articles aren't available digitally -- they are. And most are digitized in
pdf or html format. This problem has plagued me for most of my short
graduate student career. Hear me out for what I believe is a possible
My first thought was: we need a Napster for journal articles. That idea
was immediately shot down--we all know why. Then, as I was preparing my
first manuscript, I was reading through the instruction for authors and I
came upon this paragraph:
Authors may post their own published articles on their personal or
university-hosted (but not corporate, government, or similar) websites
without [publisher's] prior written permission provided that appropriate
credit is given (i.e., either the copyright lines shown on the top of the
first page of the PDF version or Copyright ⌐ [Publisher] [insert journal
name, volume number, page numbers, and year] for the HTML version).
And a search at another publisher's (Science) site reveals:
Papers may be posted after publication on not-for-profit reprint servers.
And yet another publisher's site:
From 14 February 2002 Nature Publishing Group no longer requires authors
to sign away their copyright. Instead, we are asking for an exclusive
licence. In return, authors will be free to reuse their papers in any of
their future printed work, and have the right to post a copy of the
published paper on their own websites.
In addition, authors - and the institutions in which they work - will be
free to use their papers in course packs.
I am allowed to publish (i.e. put it on my own website) my written work on
my own website (and why shouldn't I?)! As an aside, copyright of
biomedical journal articles work almost like music -- the authors sign away
all copyright ownership to the publisher (for most publishers). So these
paragraphs were music to my ears! Rather than have a Napster-like utility
to trade the actual pdf or html files, all we require is a Napster that
trades URLs which point to where these articles can be found. This type of
URL publishing is not new -- a google search on RSS/RDF will show this. This
is such a simple solution that there must be someone, some project out
there that is already implementing it.
----- end of post -----
I submitted this months ago and was milling about whether or not I should start this service on my own. Alas, I realized that the possible benefits of this service to the public far outweighed my selfish desire for monetary gains. This type of service is very simple to implement at pmbrowser.info or at nodalpoint. All they need is an additional module that allows original authors of papers to submit URL's to their papers on their personal website. For example, Holcombe or Eagleman, surfing through pmbrowser.info or nodalpoint could submit their paper published on their personal website. And when a user searches for their article at either pmbrowser.info or nodalpoint, the URL to that paper is returned along with all the other information that PubMed supplies. Heck, an even simpler hack would have the author submit the URL as the first comment in the forum -- thus allowing each subsequent reader to be able to read the paper in its original form (and more if the author wishes) and then allowing a public forum for online commentary in the same place!
I would definitely like to hear your thoughts on this proposal. As a matter of fact, if you need help hacking up the module to implement this service on your site, let me know.
If you use PayPal and have linked a banking account to your PayPal account, be absolutely careful. PayPal just started with a new policy of forcing users to link to a valid bank account from a valid bank, which doesn't include Internet banks such as NetBank -- hence, if you want to do business on the web and need to link to a bank account, I suggest you open an account from your local bank far removed as possible from a banking account that you use for your normal everyday needs (i.e. the account that you have money directly deposited from your place of employment). Read the following and you will see what I mean:
If there are insufficient funds in your PayPal balance, you agree to reimburse PayPal through other means, as described in the Payments (Sending, Receiving, and Withdrawing) Policy. Furthermore, if you open a Premier or Business Account after October 11, 2001, you authorize PayPal to debit your bank account linked to that PayPal account for the amount that you owe PayPal on transactions which were not covered by the Seller Protection Policy and which were not recoverable from your PayPal balance.
PayPal will not hesitate to drain your bank account to fund reversals of credit. This is some dangerous s#*@! By agreeing with their new policy, you're giving them a carte blanche approval to tap your funds. Before, they had to kick and scream for you to issue a check in the likelihood that you owe them money, but now...no go, they'll go straight to your wallet without asking you (beyond you agreeing to the new terms). So be careful! You've been warned!
Two behind the scenes upgrades were made to this blog. Apparently, my fiddling with the news feeds for this page took a toll for user access. Everytime this page was loaded by a new visitor, the script had to directly access the remote RSS files to display the news headings. The problem with this type of access was that my site's ability to be displayed in a timely manner was dependent on the availability of the remote RSS/RDF files. Well, this was a bad system of handling newsfeeds. I've now resorted to caching the RSS/RDF files every 2 hours and this has improved access time noticeably.
Secondly, I've now resorted to using BlogRolling.com to handle links to fellow bloggers. The service compiles my links and spews out usable code (in my case I'm using a RSS file) for me to use in my blog template. As you can see under "Fellow Bloggers," I've added a few additional sites. Honestly, I'm trying to increase my value at blogshares.com to get listed for trading. We'll see where all this blogshare trading leads -- for all we know, this blogshare service could go by the wayside and be sent to the big blog in the sky.
AVERATEC Rebate Inquiry - Search. Was sweatin' it a little bit, but I just deposited my $150 rebate check from BestBuy and looks like the $50 rebate is on its way. Glad to see that the rebates for my laptop were issued as promised. This further bolsters my recommendation for getting this laptop or this laptop.
Just came across an amazing story about a hiker whose right arm was unfortunately pinned by a large boulder while trekking alone in Utah. He stayed pinned for 5 days! He had to amputate his arm with a dull pocket knife to free himself to safety. Just amazing.
Eagleman & Holcombe proposal. May 1st issue of Nature printed a letter from the above two authors. Although their proposal is not as extensive as TrackBacking implemented at www.pmbrowser.info, it is a possible first start -- baby-steps to get scientists entrenched in the "old ways" to get with the times. I wonder if the two authors of the letter knew about www.pmbrowser.info?
I have a few points of contention with their proposal. First, there is no need for a designated moderator. If there are just as many users/readers of PubMed as there are of Slashdot, the users can self-moderate just like at Slashdot (and at Amazon as mentioned); however, the model depicted by Slashdot is better in that all comments are recorded and readers can set their "threshold" to a certain moderation level to browse/read/peruse the comments, rather than have comments completely deleted from the system. In fact, if the powers that be at the Community of Science worked together with PubMed organizers, we can have a system that minimizes libellous comments, i.e. reduces the number of anonymous posts. Second, it makes no mention of the blogging movement and its potential benefit for the scientific community. And lastly, individuals with limited access to the Internet and researchers without the funds to subscribe to all their relevant journals will be left out in the dark. Think about it, we have to have access to the papers to read prior to placing comments or reading other people's comments -- it's like going to journal club without having read the paper.
Allowing a common, well-known area for public comments of published papers is a "no brainer." I feel that problems within the scientific publishing industry have to be solved before the true benefits of this action are reaped. More specifically, until access to papers become easier for everyone, the benefits of a comments board will be minimal. I concede that my views may be extreme; however, I see the scientific publishing industry coming to a crossroads that the music industry underwent in 1997 when Napster came to the forefront. The publishing industry has to decide now whether to go down the same road that the music industry did, or they can pave the way for better and cheaper access and be leaders rather than followers and ultimately dinosaurs of the past.
Google Search: cinco de mayo. Although it's a holiday commemorating a momentous occassion for Mexicans, Cinco de Mayo, I still feel, is just another excuse for us Americans to binge drink (or so Corona would like us to). For most Americans who have no Mexican ethnicity, it's just another excuse to get red-faced -- no different than St. Patrick's Day or Mardi Gras (just to name a few, think of any others?). Anyone care to admit they celebrate Cinco de Mayo, and why?
HubMed Citation Finder. Have you ever come across a paper with a citation list that you wanted to import to your bibliography manager? Some of you may be lucky enough to be reading the article on the publisher's website. The site may by chance have a quick link to download all citations in a format that you can import into your bibliography manager. If that link is not available, you could always manually search for every single citation at PubMed (via your bibliography manager), but for those of you who want to work smarter than that, read on.
The link that I provide above is to a tool called Citation Matcher. All you need to do is drop text into that box of ALL the citations that you want to collect for your bibliography manager, submit and click forward through the tool. The last page that you encounter will be a listing of all the citations you wanted and at the bottom, buttons from which you will choose, regarding the format of the downloadable file, to import into your bibliography manager.
You may wonder, "How is this different that doing it manually, I still need to type in the text of each citation right?" Again, if you're astute enough, you don't have to type it all manually. You can just copy and paste from the paper's website (via the publisher) or if you have a PDF file of the paper, you can use the "Text Selection Tool" (that's the button with the big T) to select, copy and paste your text into the Citation Matcher tool. Hope this makes you a more proficient student/researcher. Comments, complaints, or glitches with this tool? They're welcome as always.
BlogShares - The Struggling Grad Student. Hmmm....due to the sudden high number of hits I've seen for my site, I decided to peruse my visitor IP log to see if there was some glitch in my code/site. While looking through the log, it appears that a number of search engines are crawling through, some quite often. I came across a rather interesting search engine -- blogshare (link above). Actually, turns out that blogshare crawls through blogs specifically and is not a search engine in the traditional sense. Just so happens that my blog has a "value." Sure, it's a fictitious game, but if I generate more traffic, I should theoretically see my value go up! Help make this site successful by doing any of the following: 1) place a link to my site in your blog, 2) just come by and visit/read sometime, 3) comment and trackback as often as possible, and 4) if you're a registered blogshare user, buy some of my blogshare. I promise that it'll be worthwhile, with lots of goodies to help you through your day (especially if you're a scientist in the field of biology/medicine). Hopefully I'll be able to keep this up for a substantial portion of my life -- time and money will dictate. I've got a few more topics to blog about today and will split them up to be a little more organized. Notice that now, since I'm listed at blogshare, I have a little icon on the left signifying this.
Online or Invisible? [Steve Lawrence; NEC Research Institute]. I'll let you digest information about the benefits of open access to scientific literature. First sentence of the article: Articles freely available online are more highly cited. For greater impact and faster scientific progress, authors and publishers should aim to make research easy to access.
It seems like Starbucks learned this fact long ago -- have stores easily accessible, i.e. have them everywhere and still make money. Why are we scientists still stuck in the Ice Age of literature access? Are the publishers too greedy? Looking at the cold hard facts -- scientific progress will most definitely advance with easier, less cumbersome access. Why isn't the advancement of science the first and foremost priority? Talk amongst yourselves, I'm all vaclempt!
Time is flying by. I can't believe the work is piling on. Got to have an abstract in by tomorrow afternoon, a paper out, and start working on a presentation that I'm scheduled for the end of the month. No fun sitting in the lab Sunday afternoon -- I'd much rather go have fun with my son on this beautiful day.
Public Library of Science. Just got an email in my inbox about the start of a new journal at the Public Library of Science. The following is the text of the message:
Date: Fri, 2 May 2003 02:39:26 -0700
From: Public Library of Science
To: John Vu
Subject: Public Library of Science Journals
The Public Library of Science initiative, an international grass-roots
organization of scientists, is launching its first open access journal. PLoS
Biology will compete head-to head with the leading existing publications in
biology, publishing the best peer-reviewed original research articles, timely
essays, and other features. We will begin accepting papers on May 1st.
By signing the PLoS open letter, you helped create this journal and the other
PLoS journals that will follow. Let's work together now to make these journals
We need your help to ensure that every scientist in the world knows about PLoS
Biology. Please join our grass-roots network of PLoS Advocates to spread the
word abut PLoS at your institution, and encourage your friends and colleagues
at other institutions to do the same. Visit http://www.plos.org/cgi-bin/advocates.pl to sign up.
As a first step, we have produced simple posters promoting PLoS and announcing
the launch of PLoS Biology (available at http://www.plos.org/posters.html).
We'd like to see these posters in every hallway, elevator, bulletin board and
cafeteria of every university and research institution in the world, so please
print them out and hang them wherever you can.
Please also take the time to tell your friends, colleagues, and students about
PLoS. Include an "I Support PLoS" slide in all of your talks and add a PLoS banner to your website (these can be obtained at
http://www.plos.org/support/stuff.html). If you hear about a great piece of
research, tell us about it and encourage the authors to submit it to PLoS. And,
of course, submit your best work to PLoS Biology!
As always, we welcome your ideas and suggestions.
Harold E. Varmus
Patrick O. Brown
for Public Library of Science (firstname.lastname@example.org)
P.S. For a future poster, we would like to assemble a photomosaic of scientists
around the world who support this initiative - if you send us a small digital
image of yourself (less than 100kb), we will include it.
Please pass the message on. Blog it, comment it, trackback it. Do whatever you can to make this venture successful, the future of open access biomedical literature depends on it.