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Great apps for Scientists!

smueboy

smueboy

macrumors 6502a
Original poster
Oct 30, 2006
778
1
Oz
Browsing around today i found THIS website, which is a great resource of cool little apps for scientists (made by scientists). [What was funny to me is that i know their lab and their work since it is my field]

What caught my eye was Papers, an app for organising you library of PDF files into folders and categories and adding notes and ratings etc. to each one. It's still in beta, but it looks exactly like something i need! (if anyone knows of a similar program i'd love to hear about it). Endnote has never been a reliable way of storing all of my pdf files, but Papers seems to be an iTunes-like answer to the problem.


I also downloaded another app from the website called LabAssistant - which looks like a science-based version of iCal to organise you time and notes throughout the day.

Lastly, their Solutions widget looks pretty cool for calculating molarity etc.

:)
 
Thanks for the links, I'll be sure to check them out. It's good to see there's a community of scientists here, and out there making Mac-apps for us. :)
Do you know of any good 1-D Poisson solvers for OS X (for doing things like calculating band profiles in semiconductor devices)? Maybe it'll be a google project this afternoon.

Thanks again.

Edit: just went to the site, it looks pretty professional, I might say. Also, since you're evidently also a molecular biologist, I'll assume I need to find that Poisson solver on my own. :p
 
great, thanks, i was just looking for something similar to the PDF explorer under windows, this papers really seems fit. lol, wish it would be a freeware, but.....anyway, its good


how can i import my papers? i got several hundreds, i can't import it one by one???!!!, how to add a folder and make it automatically import all papers in the folder?
 
smueboy said:
What caught my eye was Papers, an app for organising you library of PDF files into folders and categories and adding notes and ratings etc. to each one.
Click to expand...
Definitely sounds like a a nice iTunes like thing for PDFs which can only be a good thing.

For me, the downside seems to be that it is tied to sources of papers (PubMed) that are less useful for me, perhaps the author should link to something more general as well like http://scholar.google.com

B
 
clevin said:
how can i import my papers? i got several hundreds, i can't import it one by one???!!!, how to add a folder and make it automatically import all papers in the folder?
Click to expand...

You can drag many PDf's into it at once - but if you want to match the PDF to a citation from PubMed, you need to do it one by one and then add them to groups (or create smart groups). Time consuming, i know. :( I can't see how else i could be done (pulling the info from the pdf and automatically finding the citation seems too hard for the program).
 
Thanks everyone for the links. I switched to a Mac back in November and have been looking for decent science software for it. I've got e-reams of journal articles in PDF that I think Papers could really help with.

I'm also checking out the EnzymeX since I have several PC versions of similar software that I'm running via Parallels but would like something that's native to OS X.

:)
 
smueboy said:
You can drag many PDf's into it at once - but if you want to match the PDF to a citation from PubMed, you need to do it one by one and then add them to groups (or create smart groups). Time consuming, i know. :( I can't see how else i could be done (pulling the info from the pdf and automatically finding the citation seems too hard for the program).
Click to expand...

lol, no, i was saying my pdf file is in different level of alot of folders, reference/journal/volume/*.pdf s. i was hoping i can just add "reference" folder, and it will discover all my pdfs in sub-folders. lol, apparently it can't
 
clevin said:
lol, no, i was saying my pdf file is in different level of alot of folders, reference/journal/volume/*.pdf s. i was hoping i can just add "reference" folder, and it will discover all my pdfs in sub-folders. lol, apparently it can't
Click to expand...

yeah - i knew what you meant because i have similar directories and tried to do that too. Plus, when you make a group and try to add pdf's directly to that, it only adds them to the library and not the group (you need to do that after importing).
Still, it's beta, and hopefully they'l fix that by the time 1.0 gets here.
 
wordmunger said:
Endnote also does similar stuff, plus helps you track citations.
Click to expand...

endnote is, IMO, the worst piece of software i've ever used...not b/c it doesn't do what it's supposed to do, rather b/c of the company's awful upgrade pricing...too many "major" updates with no free upgrades...fine if you have a university license, but not fine if you're buying it personally.

for now i'll stick with mellel and bookends, which are far better than word/endnote!
 
smueboy said:
Browsing around today i found THIS website, which is a great resource of cool little apps for scientists (made by scientists). [What was funny to me is that i know their lab and their work since it is my field]

What caught my eye was Papers, an app for organising you library of PDF files into folders and categories and adding notes and ratings etc. to each one. It's still in beta, but it looks exactly like something i need! (if anyone knows of a similar program i'd love to hear about it). Endnote has never been a reliable way of storing all of my pdf files, but Papers seems to be an iTunes-like answer to the problem.


I also downloaded another app from the website called LabAssistant - which looks like a science-based version of iCal to organise you time and notes throughout the day.

Lastly, their Solutions widget looks pretty cool for calculating molarity etc.

:)
Click to expand...

DUDE...this is awesome. Sorry, but you have no idea how long me and my fellow post-doc have been looking for some sort of software to do this. The Papers program is amazing and is going to help out a lot. Thanks!
 
wordmunger said:
Endnote also does similar stuff, plus helps you track citations.
Click to expand...

Endnote's handling of PDF's always annoyed me. The concept of a PDF database seems pretty obvious but papers is the first i know of.
 
Looks nice. I've been watching them for awhile and have been waiting for something useful. Hopefully they will add more search engines besides pubmed. I prefer web of science. It will be nice to watch this app mature though. I hate endnote, but its pretty much all there is out there now.

Some other links people might find useful:
Scriptome - clever name. A repository of perl scripts for common biological uses.
Hyper Jeff - Not specifically just for science, but has a very nice db of apps including a good science section.
 
Spotlight made my last two years at Uni so much better. Being able to search through pdf files of journal articles for the exact phrase or formula made everything easier.

Shame I'm not at Uni any more to try these out but I'll bookmark them just in case.
 
For those outside the beta-field of research (epidemiology for instance), it would be worthwhile to check out http://www.r-project.org/. R is an open source programme that can do pretty much everything SPSS can handle....for free. There's an OSX version as well.
 
Thanks for the link! I start Grad School in September and that Papers progam will be really useful.

Does anyone know a good program for graphing and analyzing data for Macs?
 
I'm still waiting for the OriginLabs folks to release a version for OS X, because I find it to be the best program for data analysis that I've found.

Having said that, I use Kaleidagraph for my 2-D plotting needs, and DeltaGraph seems to be a worthy alternative as well.
 
That Papers looks really nice!
I have been using Yep until now for organizing my PDF's. It's pretty good as well, but this looks more full-featured, and then it's cheaper...
 
I've been using EnzymeX and 4Peaks from those guys for ages - they're excellent. Occasionally they crash, but they are generally very stable, look good and most importantly, they're very functional. EnzymeX is very good for building plasmids, looking for restriction sites in your DNA sequence etc.

heheh, "mekentosj" - those crazy Dutch... :p
 
I also think that the Papers app looks nifty. I tried using it, but it doesn't seem to be quite functional enough at this point for my uses.

I have a few hundred journal papers saved as PDF files in a folder. Right now, whenever I need to search for a paper, I do a Spotlight or a Finder search for an author name, keyword, etc. Most of these are from chemistry and engineering journals and often don't show up in PubMed, so I'd really have to wait for the developers to implement some modules for other, more general databases like ScienceDirect or ISI.

I'll definitely be keeping an eye on this piece of software.
 
kugino said:
endnote is, IMO, the worst piece of software i've ever used...not b/c it doesn't do what it's supposed to do, rather b/c of the company's awful upgrade pricing...too many "major" updates with no free upgrades...fine if you have a university license, but not fine if you're buying it personally.

for now i'll stick with mellel and bookends, which are far better than word/endnote!
Click to expand...
Amen to that. I was hesitant to switch to Bookends (and I still have Endnote on my Mac), but I'm so glad I did. Just the ability to drag and drop from PubMed to my library was worth the cost to switch! And the whole program just feels more "Mac-like" to me.

Thanks for pointing me to the mekentosj site! EnzymeX alone is going to save me a lot of headaches. Does anyone know of a similar program I could use to draw DNA vectors? If I have to get DNAStar I will, but I'd rather save the money...
 
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