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Post Archive
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August (1)

Wednesday Micro Hits
Wednesday, August 17, 2011
July (1)

Is it worth getting an education?
Thursday, July 7, 2011
June (2)

Miscellany
Tuesday, June 28, 2011

It Gets Better
Thursday, June 2, 2011
May (4)

Wednesday Micro Hits
Wednesday, May 11, 2011

My first experience with science writing (Part 1 of 2)
Tuesday, May 10, 2011

This is why we get vaccinated
Thursday, May 5, 2011

Monday Morning Jam
Monday, May 2, 2011
April (2)

Saturday Morning Serenade
Saturday, April 23, 2011

So long, farewell ...
Friday, April 1, 2011
March (10)

Stay Tuned ...
Thursday, March 31, 2011

From the Union of Concerned Scientists
Tuesday, March 15, 2011

Week 23 - Hockey Pool
Monday, March 14, 2011

March Madness
Monday, March 14, 2011

Saturday Morning Serenade
Saturday, March 12, 2011

What a bargain!
Wednesday, March 9, 2011

Wednesday Micro Hits
Wednesday, March 9, 2011

Technique Overload
Monday, March 7, 2011

Saturday Morning Serenade
Saturday, March 5, 2011

Et tu FDA?
Wednesday, March 2, 2011
February (10)

Saturday Morning Serenade - A Hip Edition
Saturday, February 26, 2011

Saturday Morning Serenade
Saturday, February 19, 2011

Wednesday Micro Hits (on Thursday!)
Thursday, February 17, 2011

HR1
Wednesday, February 16, 2011

Happy Valentine's Day
Monday, February 14, 2011

Saturday Morning Serenade
Saturday, February 12, 2011

The GOP War on Science
Wednesday, February 9, 2011

Wednesday Micro Hits
Wednesday, February 9, 2011

People, how about some ...
Tuesday, February 8, 2011

Saturday Morning Serenade
Saturday, February 5, 2011
January (21)

Saturday Morning Serenade
Saturday, January 29, 2011

Sacrifice
Friday, January 28, 2011

Are you married to your reagents?
Thursday, January 27, 2011

Wednesday Micro Hits
Wednesday, January 26, 2011

Common Sense Tip #1
Tuesday, January 25, 2011

Saturday Morning Serenade
Saturday, January 22, 2011

From the Baby Boomers, a Big "Screw You"
Friday, January 21, 2011

Student Worker - More Student or More Worker?
Friday, January 21, 2011

Wednesday Micro Hits
Wednesday, January 19, 2011

Saturday Morning Serenade
Saturday, January 15, 2011

Holy moly!
Friday, January 14, 2011

Thursday Pondering
Thursday, January 13, 2011

The Electronic Office
Thursday, January 13, 2011

Wednesday Micro Hits
Wednesday, January 12, 2011

Saturday Morning Serenade
Saturday, January 8, 2011

The Plug - January Edition
Friday, January 7, 2011

Bits 'N Pieces
Thursday, January 6, 2011

Latest Manuscript Review
Wednesday, January 5, 2011

The $4 gallon of gas
Wednesday, January 5, 2011

Our slowly shrinking (and dying) planet
Tuesday, January 4, 2011

It's 2011 already? For reals?
Monday, January 3, 2011
2010 (46)
December (9)

Saturday Morning Serenade
Saturday, December 11, 2010

The State of Microbiology
Thursday, December 9, 2010

Wednesday Micro Hits
Wednesday, December 8, 2010

2010 blogging meme
Tuesday, December 7, 2010

The Environmental Impact of the Christmas Season
Tuesday, December 7, 2010

Music Snobbery
Thursday, December 2, 2010

Phantom Power
Thursday, December 2, 2010

What's Your Name?
Wednesday, December 1, 2010

Wednesday Micro Hits
Wednesday, December 1, 2010
November (8)

Saturday Morning Serenade
Saturday, November 27, 2010

Awakening from the food coma ...
Friday, November 26, 2010

Wednesday Micro Hits
Wednesday, November 24, 2010

Donor's Choose Final Followup (Recipes #3 and #4)
Tuesday, November 23, 2010

A Monday Mess
Monday, November 22, 2010

Saturday Morning Serenade
Saturday, November 6, 2010

Wednesday Micro Hits (Peer-Review Edition)
Wednesday, November 3, 2010

Day 2 of the ASA-CSSA-SSSA Meeting (#ACSMtg)
Wednesday, November 3, 2010
October (29)

ASA-CSSA-SSSA Meeting - Day 1
Sunday, October 31, 2010

Stayin' Alive
Sunday, October 31, 2010

Saturday Morning Serenade
Saturday, October 30, 2010

Wednesday Micro Hits (Vol. 4)
Wednesday, October 27, 2010

ASA-CSSA-SSSA Early Career Program
Monday, October 25, 2010

Saturday Morning Serenade
Saturday, October 23, 2010

Wednesday Micro Hits (Vol. 3)
Wednesday, October 20, 2010

Donor's Choose - Family Recipe Number 1
Sunday, October 17, 2010

Making Good on Donor's Choose Bribe - Comfort Food Recipe 1
Saturday, October 16, 2010

Saturday Morning Serenade
Saturday, October 16, 2010

Friday Wrap-Up and Random Thoughts (Vol. 2)
Friday, October 15, 2010

First I Begged, Now I Bribe
Thursday, October 14, 2010

Finding Out Things The Hard Way(TM)
Wednesday, October 13, 2010

Wednesday Micro Hits (Vol 2)
Wednesday, October 13, 2010

Here's where I start begging ...
Tuesday, October 12, 2010

#UnK3rn3d: Life Outside the Lab?
Tuesday, October 12, 2010

First fleas, now frogs?
Tuesday, October 12, 2010

No Fleas Please
Monday, October 11, 2010

My next Research Blogging article has been chosen ...
Sunday, October 10, 2010

Saturday Morning Serenade
Saturday, October 9, 2010

Donor's Choose
Friday, October 8, 2010

Friday Wrap-up and Random Thoughts
Friday, October 8, 2010

RB: Waste Not, Want Not.
Thursday, October 7, 2010

Research Blogging
Wednesday, October 6, 2010

Wednesday Micro Hits
Wednesday, October 6, 2010

What if I were not a microbiologist ...
Tuesday, October 5, 2010

TJ's Tips on Manuscript Review
Monday, October 4, 2010

Chinese plagiarism and the death of English-language journals
Friday, October 1, 2010

Allow Me a Formal Introduction
Friday, October 1, 2010
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Thomas Joseph

It's a Micro World after all is a blog dedicated to discussing pretty much whatever I feel like. When I delve into scientific matters it will primarily be discussing microbiology (agricultural, bioenergy, and environmental focus). Otherwise, I'll probably ramble on about sports and life.

My posts are presented as opinion and commentary and do not represent the views of LabSpaces Productions, LLC, my employer, or my educational institution.

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Awesome Stuff
Thursday, January 13, 2011

These are tough times. Everywhere you look money is tight, budgets are stagnant or shrinking, we're being asked to cut costs, and incorporating money saving methods to keep those costs down are becoming commonplace. I started out 2011 (actually ended 2010) intent on doing my part in not only cutting costs in the operation of my lab/office, but greening them up as well.

As I looked about my office there was one thing that jumped out at me. The volume of paper which was cluttering my desk and shelves (I actually have a set of metal shelves I purchased two years ago to hold all the scientific papers I've printed out in the past several years).

Paper, paper, everywhere,

Until all the trees were dead.

Paper, paper, everywhere,

Nothing interesting to be read.

Coleridge, if he had ever seen my office.

Between the cost of paper and the price of ink, I imagine that I have spent a lot of institutional money printing out versions of my manuscripts, other peoples scientific papers, progress reports, and other assorted stuff. It all adds up over time.

I'm not sure how much my institution pays in paper and ink costs each year (though I'm going to ask), but I'm sure it's significant. As such, it seemed like an "easy" thing to tackle. Now, I placed easy in quotes because I'm a big fan of reading hard copy papers, and I know habits are a hard thing to break. However when reviewing manuscripts I'm often writing notes in the margins only then having to go back over to Word to then type them in. So why not skip the pen/paper middleman?

The same goes with manuscript revisions. I think "track changes" is one of the most annoying, albeit useful, features in Word. Same goes for the "comments" feature as well. By committing to these practices, I've now effectively handled paper wasting related to the manuscript review process (both my own, and for others I review). However, what to do with science reports?

To address this issue, I relied on a couple of programs I already had on hand.

1. EndNote (version X3)

2. Adobe Acrobat Pro (version 9)

Now, going out and buying EndNote won't help you cut down on your bottom line ... at least for the short term. Same goes for Adobe Acrobat Pro. However if you have them on hand, or can find freeware (or cheaper) software which does that which I will explain ... go for it! For example, I know there are two programs which go by the names Mendeley and Papers which (from what I've heard) are both great reference managers and come at no to minimal cost. I know of no alternative for making comments in PDFs than Acrobat Pro (can someone offer any alternatives)?

I used to use EndNote simply to insert references into manuscripts, but since it can also link to PDFs on your hard drive (and in my experience can pull down ~70% of all PDFs it searches for from the internet), it becomes a great office tool as well.

To date I've managed to collect over 1,100 PDFs into EndNote. I've joked with co-workers that if we ever lost our internet connection for an extended period of time, I'd likely be one of the only scientists who'd be able to write their papers because all of them are neatly saved to my desktop. If you figure an average of 10 pages per report, that's over 11,000 pieces of paper (5,500 if I print front/back) that won't need to be printed out. Of course that number is going to increase as the year progresses.

The other beauty of EndNote is that, like iTunes, you can create labels within each library and even use a smart search to create labels under which particular papers (i.e., anything with "anaerobe in the title", or "Smith, AB as author") will automatically be filed. Also, the fact that it interfaces nicely with Scopus, PubMed, Web of Science, and even Google Scholar means that pulling your favorite papers off the internet are rather simple. EndNote X4 which is even sweeter allows you to drop and drag a PDF into EndNote. Once dropped, EndNote grabs the DOI number and fills out a new entry automatically ... so if you have access to the PDF, you can skip the import or "add a new entry" step altogether.

Obviously I won't be able to stop printing paper altogether. There will be instances when it's necessary ... however with fillable PDFs, and electronic signatures, those times can (if one commits to the practice) be few and far between. I'm almost halfway through January and I have yet to print anything out for work (and I've been at work since the beginning of the year, so it's been a legit almost two weeks of official work).

So why? Well, I've spent a lot of time talking about the need to be more conscientious of our environment, of not wasting resources. I think it'd be somewhat hypocritical on my part to ignore resources that have been made available to me that would allow me to "green up" my work environment and lifestyle, even a little bit (and every little bit helps). Taking steps to reduce vampiric power consumption, reducing food waste, and now reducting my ink and paper consumption are the steps I'm incorporating to reduce my overall carbon footprint. Next I'm going to tackle my daily commute, but for now I'm going to look into how to make my office that much more electronic (without the need to buy expensive and/or flashy hardware ... which is going to be an even bigger temptation because I'd love me an awesome tablet like the Toshiba Honeycomb).

Has anyone had experience with an electronic office? Tips and tricks would be more than welcome.

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Genomic Repairman
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I have been rarely printing my papers lately so much so that my printer has gathered a nice layer of dust.  I use Papers but can't put notes directly to the PDF but in a side category that sits next to it and is easily accessed.  Once I get my new MacBook, I think I'm going to test out your method if it seems to be working well for you.


Suzy
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Wow- that's pretty good- not printed anything?

One change I am considering, for lab meetings, everyone makes printed copies of their lab experiments for everyone to have while we discuss it. I am thinking of instead using the projector and just discussing the data on the screen instead of on paper.


Thomas Joseph
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GR, I'll keep you updated.

Jade, well I had to print out four copies of a one page scientific commentary piece to share with collaborators today. The first four pages I've printed out all year (other than the insurance info for my car). Using the projector would work ... and if your coworkers bring laptops with them, you could print your data into "Adobe PDF" format and email it to them, allowing them to view it on their laptop screens alongside the projector.

We do alot in PDF format at work, especially on the IT side (I'm now instructing others at work on how to use EndNote). A program called Snagit (version 10) works very well in allowing me to show people what they should be doing, step by step, when setting up their libraries, downloading PDFs, etc. Screen grabs are a pretty good tool (especially if your image doesn't need to be pretty-fied).


JaySeeDub
Dub C Med School
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CutePDF and OpenOffice both also allow commenting on .pdf's.  Both are a little clunkier than Adobe Pro's inhouse commenting and editing, but if you don't want to shell out $125-300 for Pro then learning to work around their awkwardness would be a good idea.  Personally, I prefer PDFedit, but that requires a *nix native or *nix-like environment, like Cygwin.  Since a lot of my academic stuff is done on a slackware box, it works great for me.  If you can type fast, faster than most people can manipulate a mouse, then PDFedit may be an even better solution since it's all command line.

Other solutions include Foxit (which really only allows annotation and adds a watermark), A.nnotate (web based), Idea Rover (Windows only and saves edited pdf as a .docx) and KNote (has an awesome encryption feature, but incredibly steep learning curve).

 


Thomas Joseph
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Thanks JaySeeDub. FoxIt looks like a viable, free option for PDF commenting.

I forgot to add this one limitation to the Electronic Office and PDFs. Some journals "lock" their PDFs which means you cannot make comments, highlight, etc in them. That is extremely annoying. There are a couple of journals I've run across which do this.


JaySeeDub
Dub C Med School
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Yeah. I got in trouble for showing people around the med school how to undo the locks on PDFs. They're actually not very secure, and there are a few cumbersome programs that will "unlock" the .pdf for you by making a new copy without the password. I never understood adding a password to .pdfs because if you know where to look there's a line that says pass="whateverthepasswordis".


Suzy
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and where would that be?


Thomas Joseph
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Yeah, where would that be?  Also, I believe another work around is to "print" the PDF back into PDF format. I'll have to give it a shot and see if that works.


JaySeeDub
Dub C Med School
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Easier way is via Hack-5, my way involves opening the .pdf in PDFedit.


Genomic Repairman
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And is this why you are meeting with the disciplinary board?


JaySeeDub
Dub C Med School
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No. That's because an Attending was excorciating a fellow med student on the floor in front of patients, nurses, other students, etc. I suggested that such a public venue wasn't the proper place to do this, and he told me to "shut [my] ass up, or [I'm] next." I promptly got in his face and told him to take it somewhere private or I would clock him.

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