I see a number of methods of keeping track of papers and web-pages. For papers, I see people creating folders, downloading the pdf files and trying to come up with some sort of reasonable naming system. For web-pages, I see most using bookmarks in their browsers which usually becomes unruly despite creating sub-folders.
I enjoy having access to information from any computer, which is impossible using the above methods. A number of alternatives exist such as using Delicious, FriendFeed, DropBox? or CiteUlike. (drop a comment if you have another favorite)
Derek notes that there have been a couple of worthless papers published in scientific journals. I see this as arising from a deeper issue (move over Dr. Phil) of others generally discouraging innovative ideas.
Regurgitate this information cause it’s on the test, get a paper published so you can graduate, get a grant funded so you can get tenure… just like everyone else… anyway.
I would argue that research and therefore the resulting papers won’t be considered worthless if they are remarkably innovative:
1) Remarkable innovations don’t have a road map.
2) Cutting edge is a requirement. The edge isn’t a place to be nervous; it’s where you have to live.
3) Science progresses. Innovative research is in the moment. Getting scooped isn’t a sign that you had a good idea – if your idea is half decent someone will do it, eventually.
4) Remarkable research isn’t up to you. Everyone thinks that their kids are cute, smart, etc… Is the idea worth spreading? Am I sending this paper to colleagues who didn’t ask for it?
5) Reminder: If your protocol is from a published paper, manual, textbook – it’s been done. The path to innovation is one that you blaze.
6) Most people don’t even try for remarkable innovations so don’t expect much support. Actually, expect resistance, it’s easy to defend the norm.
7) Are people excited? Do they look forward to putting in the work? Everyone isn’t going to believe in your work or idea, but a few will certainly help.
Remarkable innovation isn’t putting fellatio in the title of your paper. Getting attention isn’t remarkable.
9) Having your paper cited is a sign of being remarkable, just make sure it’s not just you.
10) If high impact factor means Nature, you are missing the point.
Magic happens during poster sessions. We are able to ask questions, share stories, set up collaborations, make friends and see old faces.
A growing trend in poster sessions is taking photographs. Photos save time and can serve as nice reference for those scribbled notes after the conference is over. I see conferences as being about people so may I suggest getting to know the presenter and not just asking for a picture. As a side note, please make sure to GET PERMISSION from the presenter before taking a picture.
Photographs will keep gaining popularity especially with the use of camera phones.
So let’s say you are attending a conference and you come away with 25 pictures of posters (this could also be done of presentation slides) that you found interesting. The next step would be to painfully go through the pictures and try to dig up the pieces of information you had found interesting.
There’s an easier way.
Take the pictures and upload them into Evernote. The free version of Evernote has searchable text recognition of images. Evernote is web based therefore you don’t have to download anything and can upload images while on the road. Once you have all the images loaded up, it is easy to search by keywords (you can also add tags, if you wish) to find the information you are looking for.
I took this picture of the results section of a poster with a camera phone. I then searched for the term ‘calibrate’ and Evernote was able to pull up the correct image and highlight the related search term.
The image recognition is impressive, here is a zoomed in view:
Personally, my mind is full after multiple day conferences and being able to search images by keywords (author, protein name, etc…) would be really helpful. What do you think?
The Janet Smith Lab out of the University of Michigan shows us how it is done at the APS. The bar has been raised for quick crystal transfers, nice work!
For those that love upgrading crystallographic software – today is your day (and probably tomorrow as well). PyMOL v1.3 is the first release since Schrödinger took over operations from the late Dr. Warren L. Delano.
Highlights include:
AxPyMOL: allows PyMOL to be directly integrated into PowerPoint presentation
JyMOL: allows developers to integrate PyMOL features into custom Java applications
Ability to control movie output quality
New ‘obscure’ command allows one to hide molecules/ligands for presentations
Updated ‘fetch’ command can now import electron density maps if available
The full list of additions can be found on the PyMOL website. Happy upgrading!
If your protein and crystallization conditions have more metal than Robocop then you could be in trouble. The difficulty comes when placing a metal into that blob of electron density. How do we figure out which metal to place? Factors worth considering: sigma level, distance, coordination and geometry of the interactions.
Maria and Juan bring us up to speed on the last three factors concerning metals in the PDB. We have talked about MESPEUS as being a tool for examining coordination and bonding distances. This paper (pdf, html) is a nice complement with an overview of thousands of deposited proteins.
Notes:
-Na, K and Mg show no definite residue preference (!)
-Zn has a very strong association with Cys and His
-Plots with distances between metals and N, O and S atoms
BioBar is a Firefox extension that allows for quick access to databases and servers commonly used in macromolecular crystallography. This extension simply appears above the tabs in your the Firefox browser for easy reference. I find this tool pretty inspiring and instantly had a number of ideas of how it could be tweaked (for the better) toward crystallography.
Biobar contains a text search option that will bring up structures such as by the PDB ID.
The drop down menus contain great resources many of which we have covered here such as Hubmed, Pfam and the EDS.
The tool has over 130,000 downloads and no complaints – definitely worth a look.
An oldie, but still good. The Bragg’s Law applet allows for an easy visualization of the law in action. The user can adjust the wavelength, d-spacing and the theta angle. The applet adjusts to reflect inputs as they are varied.
If you click on the details button, a small window will appear that shows how the parameters play a role in Bragg’s law. A green light (shown within the red circle) will appear if Bragg’s law is satisfied.
In this example, Bragg’s law is satisfied since the result produces (very close to) an integer (4=2*5*0.615/1.54). The background grid allows for an easier time in seeing if X ray1 and X ray2 (the blue waves in the small window) are in phase. Enjoy.
Remarkable innovation isn’t putting 
If your protein and crystallization conditions have more metal than Robocop then you could be in trouble. The difficulty comes when placing a metal into that blob of electron density. How do we figure out which metal to place? Factors worth considering: sigma level, distance, coordination and geometry of the interactions.
