There are often threads on here asking for advice on specific software packages - sometimes ones that are completely new to me! I thought it might be interesting to share what we use on a regular basis. Partly to find out what's out there, and partly to see who uses the same things as you and might be able to help...

To kick off....

I use MS Office for...the usual

Stata for data analysis (will probably also use MLwin and maybe R at some point)

Mendeley for managing paper references

Zotero as an enhanced bookmarking tool to save links/webpages (I know it can be used for bibliographies too but I prefer the Mendeley interface)

And good ol' pen and paper for note making and recording my ideas. Probably sounds daft but I can't think without a pen in my hand.

I use MS Word and MS Excel, but once I have upgraded my Mac to Lion I plan to switch to Pages and Numbers (Apple's own office programs).

I use EndNote for keeping track of literature/publications.

I use the LiveJournal blogging site to manage my to-do lists, so I can update them and see them anywhere on the move. I find this better than using pen and paper (far less losable).

I use the Prolog language to manage task-management, using a project/task management simple system I programmed myself.

And I use the free MySQL database system to build and query large-scale databases for my research. Access doesn't run on my Mac (unless under Windows emulation), and I am much happier using MySQL and writing the database queries in the SQL programming language (legacy of my first degree in computer science).

I used to use DropBox to share my files between computers and do online backups. However their recent change of terms of use terrified me (even if they were subsequently edited), and I have switched to SpiderOak, who also gave me more free Gigabytes, thanks to referrals.

I use....

- word, excel for writing and working stuff out ;-)

- mendeley for reference management (after my endnote wouldn't work with office 2010 and I couldn't afford to buy a new version).

- SPSS and AMOS for stats, I'm trained in Mplus but my uni won't buy it (would have been far more useful for my thesis though!)

- Dropbox - I did switch to sugarsync for a while because I think its got better editing functions when you can't access your actual folder, but I found that it really slowed my computer down when starting up, so I switched back to dropbox.

I use:

MS office so Excel for graphs and data handling, Word for documents (inc thesis), Powerpoint for posters
Paint for diagrams
SPSS for statistics
Refworks for referencing
Dropbox for 'sending' larger files to others

I use Word for writing, Excel for data handling and graphs, SPSS for analysis, endnote for references, powerpoint for presentations, journals are organised by my own system. Would probably have been better to learn to use a more sophisticated method. To do lists are pen and paper.

I've used matlab a little bit but find the code pretty impenetrable! I ran experiments on eprime and psyscope but under the influence of my supervisor didn't really get into coding. Wish I had now as would be much better for looking for jobs. This is one place I really shouldn't have listened to her!

======= Date Modified 25 Jul 2011 21:20:44 =======
I use:

Word for writing
Mendeley for docs and references
Read It Later for web pages of interest
Evernote for saving things that are of particular interest
Dropbox to transfer files
Spideroak for backup

My list isn't that long at the moment because I don't have any data at this early stage, but here is is: (Interesting thread!)
Mendeley for referencing, also making notes quickly from PDFs - will probably transfer these to OneNote though
PDF-viewer for PDFs
Word 2010 for writing
Trying to get into OneNote - like the look of it so far
Occasionally MindGenius for brainstorming but to be honest I prefer to do this by hand.
Google calendar (if this counts) for my diary and task lists
Dropbox for back-up

I'd say noting on pdfs is better in mendeley than one note natassia - it means its there when you open up the program and you're not switching screens etc.

I just wish Mendeley was a little further on in development - I'm using it, but its bugs seriously annoy me and I'm having to do lots of work arounds. I'm also assuming that it will go absolutely mental when I combine all my chapters.

Having used both Endnote and Reference Manager it seems that software nervous break downs are par for the course when the no of references are large and you combine documents. So if Mendeley does that too it's in good company. I do agree about the development though - there have been requests for over a year that they develop a plug in for Word 2010 64 bit but they won't even announce a timeline for when it might happen. Fortunately I'm running an older version of office on my home computer so while I can type away on my work PC, I can only insert the refs when I get home. Durrr....

Interesting to hear the popularity of online back ups. It's something I'm looking in to. I'm not entirely sold on the idea of using Dropbox after I saw this:
http://www.wired.com/threatlevel/2011/06/dropbox/
I've had a couple of recommendations of Sugarsynch, but I'd like to compare some more options.

I find Powerpoint quite useful for figures actually. When I was an RA my boss had an enthusiasm for Graphpad Prism but I found it very unintuitive and frustrating. Tables I find more stable if I work on them in Excel and then paste into Word (if they're big/complex) although the tables in Word have improved a lot over the years. They still have their moments though!

The reason why I left DropBox - and I was a paying user of it, using a lot of Gigabytes - is not because of their security failure, but because of a slightly later change of terms of use. Basically they changed their terms of use to claim all intellectual rights to data stored in DropBox, including publishing that material and translating it. This change seems to have been a mistake on their part. What they were trying to do was to claim enough rights to be able to provide their service, but they overdid things on the rights they claimed. But it was enough to seriously freak out a lot of people who rely on their creative content for financial or academic reasons: such as freelance writers and artists, and academics like me - I'm a post-doc producing new journal papers, which I had been storing in DropBox until that point.

As I said DropBox did change their terms of use back to something more suitable. But it was too late for a lot of users, whose trust had been lost, and have moved to other backup solutions.

I looked at quite a lot of the options available. I chose SpiderOak because it is totally encrypted, and even the SpiderOak people can't decrypt the data at their end. And they gave me a silly number of free Gigabytes :p

I use Microsoft OneNote for to do lists, organisation and general note taking - I type up anything important that I've written on paper.
I only use Word if I'm writing something quick that doesn't need to look good but otherwise I use LaTeX. I'm a fairly recent convert to LaTeX after Word nearly died when putting my MSc dissertation together (although it may have partly been due to my old laptop - have a nice shiny new one now).
I use Matlab for everything to do with my data i.e. processing it, plotting it up and calculating stats. Once you've mastered the basic syntax it's fairly straightforward to make it do what you want it to do (most of the time). I can only make simple graphs in Excel as the new version just looks way too confusing.
I use Mendeley for reference management and it's set to export all my references to a BibTeX file that I can use with LaTex. I did start off using onenote for references and notes on papers but as Sneaks mentioned it was a pain switching between screens so I just use Mendeley now.

All of the above is done on my laptop running Windows 7 but at uni I have a Linux desktop with a whole bunch of other stuff which I won't go into. I think I'm the only one in my office doing a lot of programming and was told that my desktop looked scary when it was running through some fairly straightforward (to me at least) code the week. I'm still a beginner when it comes to programming but I know my sup is expecting me to learn Python at some point which really does look like a scary programming language!

Microsoft Office
Matlab
Simulink
GH Bladed
Mendeley

These are my main ones.

Anyone else use Simulink or am I alone on this forum?

======= Date Modified 26 Jul 2011 13:37:26 =======
Good thread!

I use:
Microsoft Word (occasionally Pages)
Numbers (prefer it to Excel)
Zotero
iProcastrinate (for to do lists and daily goals)
iCal (for long term goals)
Timemachine for backup (I quite like it, when I'm writing I plug in my external disk and it backs up every 30 mins or so. I have a 500GB external drive and I have been using that since last September. It's getting kind of full now, so planning on getting another one from September. I also back-up super important files on SpiderOak.)

I also have a notebook for ideas, planning etc.