The Ideal Software Bundle for Scientists?

Software bundles like MacHeist have become a regular feature of the Mac landscape of late. There are plenty of good deals to be had, and plenty of discussion about the ethics of such bundles. But leaving all that aside, what would be your ideal bundle for science?

I was thinking about this the other day. Here's the list I came up with:

That comes to a total price of around $400. Give me that for $50, or even $100, and I would be a very happy — and productive — scientist. (Actually, I already have a lot of this software, so I might not be the target audience. My intention was more to come up with a package that a scientist beginning on the Mac, or with little knowledge of the available software packages, would most benefit from.)

In choosing my bundle I have tried to target a general scientist, and have not included any domain specific products. I have also tried to include a package to target each of the most common activities of a scientist: personal organization, diagramming, data storage, text editing, reading and storing literature, plotting results, digitalizing data, and writing articles.

I'm sure there are lots of programs I have forgotten, or programs listed above that others will disagree on. Post your ideal bundle in the comments, and let the discussion begin.

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Ideal software

After using the mac for two years, I have tried to surrender to Apple's philosophy and use their own installed and purchased apps where possible. So my list of additional science software to purchase is small. I also think that science life could be even simpler if all the functions of theses apps were packaged in one streamlined program. If Apple integrated Filemaker into iWork and beefed up the graphing and staTs for filemaker/numbers the needs of most scientists would be covered.

iWork*
Papers
Microsoft Remote Desktop**
Filemaker Pro 9 (lab protocols & records) (Bento doesn't suit me yet as it's not cross platform).
Data analysis: SPSS 16, Igor Pro***

Drew, I'm interested to know what advantages you find Omnigraffle offers over Keynote for producing diagrams? Also you haven't listed a stats package?

After having tried many organisation/GTD software, I also just use Leopards' mail.app, notes (for project planning), todos, and ical for appointments. There are a few bugs that Apple needs to get sorted, but it's still the best. Omnifocus is too much work for me.

*I used to use Scrivener, but recently moved all my documents into Pages. Pages is not quite as good at the raw editing stage, but I got tired of stuffing around with exports from Scrivener, and getting figures out of it. Colleages would ask me for a copy of a document and I just couldn't get it to them quickly. I use Pages Table of Contents coupled with viewing thumbnails instead. Pages is simple and elegant and lures me in to want to use it. Also of late I have also turned to Keynote for making many scientific Illustrations and posters, rather than Adobe Illustrator. Keynote actually has nice bezier curves and faster keyboard navigation. It has some limitations, but does the job most of the time. I've also replaced Acrobat Pro with Preview for most PDF production.

**For when I need to use MS windows via a terminal server.

***I have not done a lot of analysis on the mac, so I'm still subject to influence here. I also get SPSS for free. I like Aabel, but I worry it might be too limited. I wish someone would come out with some powerful science plugin for iwork Numbers, in the meantime I've made reasonable workarounds for making boxplots in Numbers.

Few ideas

I didn't know GraphClick (I previously used the open source g3data), but I like it a lot and just bought it.

I don't know DataGraph well, but I don't think it does much more than the free Plot. I'm amazed, though, that you don't have any software for plotting in 3D, because it is really a common task in both visualising data and communicating your results.

The other thing I would have liked to see is a good, simple vectorial drawing program. It looks like OmniGraffle can be twisted into that, though.

What about drawing?

A vector-drawing application such as Lineform or VectorDesigner for making figures / illustrations / schematics would also be welcome.

few more ideas

To borrow a phrase, I don't know Papers well, but I don't think it does much more than the free BibDesk.

Re: Drawing

I usually use OmniGraffle for basic diagrams, so I don't really need a vector app. But I am familiar with Lineform, and can certainly recommend it.

Drew

---------------------------
Drew McCormack
http://www.maccoremac.com
http://www.macanics.net
http://www.macresearch.org

Re: Bibdesk and Plot

I am not too familiar with Plot, so I can't really comment.

I have used Papers, and it is really a fantastic product. Maybe you can do similar things with other programs, but those that use Papers are almost religious about it. It's easily worth the 30 euro price tag.

Drew

---------------------------
Drew McCormack
http://www.maccoremac.com
http://www.macanics.net
http://www.macresearch.org

Dot?

I'm not a scientist myself, but a mere computer science student. My father is a scientist, though...

For simple vector drawings you might want to check out the open source GraphViz Dot; it makes excellent and beautiful arrow charts from a simple, expressive language. I'd be interested to hear what you think of it; for passing the advice on. Thanks.

--

Dan Villiom Podlaski Christiansen

software bundle

Yes to Papers and Omnigraffle.
I'd add a couple more:
Appzapper (for removing apps)
iChat (for sharing desktops to demo things with collaborators)
Noteshare (keeping multi-userdocs available across internet)
Snapzpro (screen shots and movies of screen actions)
Netnewswire for RSS feeds
Connotea (for online ref management)
Sente (ref manager)

Chris Upton
University of Victoria
BC Canada
www.virology.ca

Bundle for science

My ideal bundle will be something like this:

Papers

pro Fit

Pymol

Graphic Converter

But, I have to agree that most of the time the FREE (i.e. Qtiplot) equivalent software can get the job down as good as the above mentioned. Actually, I already paid for pro FIt and Papers. Pymol I compile from scratch. Then again, maybe it is that I just haven't tried most of the software mentioned above even when included in one of my macs (as has been the case for OmniGraffle).

Maybe this is not the right place for this but I miss Caffeine Software. Their PixelNhance is the best program I have ever used to modify images consistently. And it was free!

Graphing Calculator

Even though I have Mathematica 6, there are things I would still rather do in Graphing Calculator. I haven't used a new version in a while, but it has been a great program.

I'd say if your vector

I'd say if your vector Illustration needs are modest, buy iwork and use Keynote. I've been a power user of Adobe Illustrator for 10+ years and I find Keynote's bezier curves are just fine the majority of the time. Plus Keynote is great for oral and poster presentations and works seemlessly with media on your mac from iphoto, preview and iTunes.

David.

Bibdesk

I like Bibdesk a lot, specially how it stores all the data in a bib file that can be used directly from latex. I haven't really used papers, haven't had the need for it. Other software: Textmate, mactex and Omnigraffle.

power

A great cross-platform stand alone app for those of you who need to make power calculations:

g*power

OT rant on problems with Pages

This is off-topic but I feel like making these comments on Pages here anyway.

Pages has two aspects that drive me nuts. First, text characters are rendered incorrectly—the particular rendering algorithm overrides the system-wide selection set in the preference pane called Appearance. The override that Pages uses is an old, out-of-date one that makes most text look too light and thus hard to read. It amazes me that this has persisted in Pages for years. It seems like an obvious bug but my fear is that someone decided to do this on purpose.

Second, there is no way in Pages to get rid of the freaking margins. News flash—the vast majority of documents these days are never printed and screen real estate is still scarce. Note to Apple: make a menu item that gets rid of about 90% of the side and top margins. Every other word processor that can think of for the Mac has this feature. Keeping the margins visible with no option to get rid of them makes it look like the target audience is people making flyers for their garage sale.

What, no LaTeX junkies here?

For writing reports: TextMate + MacTex (light distribution) + BibDesk
For managing papers: Papers
For plotting: Plot
For making diagrams: OmniGraffle

Increasing the page size and

Increasing the page size and margins and changing the view to "Two-up" and possibly changing to two-column view goes some way toward viewing more of your document on the screen.

The Ideal Software Bundle for Scientists?

OmniFocus is one of my favs also!

Some things are free...

And some are not.

R is a great scientific package that's free. It can be a steep learning curve and isn't exactly GUI-driven, but it has an enormous number of packages written for it that probably cover most any scientific task you might have.
Igor Pro is also great and has wonderful graphing capabilities, GUI, and support, for a reasonable price.

OmniGrafffle is great for many diagrams/charts.
Graphviz is free and it's easy to output its DOT language from programs you might write. (The previous version of OmniGraffle reads basic DOT, and the latest version even incorporates several graphviz algorithms, FWIW.)

Weka and FreeMat are free.

OmniOutliner is great for outlining and outline/simple-spreadsheet tasks.

Pages is very useful, as is Preview. Numbers is elegant, but doesn't seem to perform well on anything beyond small datasets.

App Bundle for Scientists

See my app bundle wishlist.

Many applications are the same as in your or commenters' lists with one notable addition being DevonThink Pro.

P.S. I wrote that blog post first as you have to register to post comments here. This site is very interesting and I registered in the end, but what about allowing people to login using OpenID in order to post comments?

Free and Open Source Apps

Some of comments here (e.g., "Some things are free...") talk about open source alternatives which at times can be as good or even better than their commercial analogues. Anyway, they are free. :)

Maybe we need another post for collecting together application names for a "Free and Open Source App Bundle"?

The current topic could also be used, but the initial post talks about collecting together a bundle of apps that you need to pay for.

One of such apps which I've been fascinated with recently is NodeBox - it is an incredible 2D graphics app, scripted with Python. 've got to see it to believe. Now I just need to find some "serious, scientific" application for it.

A few more...

As a chemist, I have my own set of specific apps, so I'll ignore those.

People have already posted many of my favorites: OmniOutliner or DevonThink, OmniGraffle, OmniFocus...

Here are some general ones...

  • Adobe Acrobat (which includes OCR for PDF files)
  • Keynote. If you're a Mac user and still running PowerPoint, your presentations will improve quickly.
  • Grapher. It's incredibly useful for quick mathematical plots.
  • Typinator or TypeIt4Me. Save yourself keystrokes and fix typos as you type.
  • Quicksilver or Butler or LaunchBar -- so much more efficient.
  • SnapzPro or other screencast solution

Two nice (free) TeX programs...

A couple of people have mentioned TeX, but I think they mentioned non-free programs.

I've been using two free programs lately that both work very well:

1. The TeXShop package includes everything, including TeX/LaTeX/etc, and four other programs:

The TeXShop editor, which is a nice, syntax-coloring text editor that includes macros, lots of options, and it will work with TeX, LaTeX, XeTeX, ConTeXt, etc, etc. It has synchronization with the previewer (CMD-click on text in one to see it highlighted in the other), and is an all-around nice solution if you're a power user or like to be close to the LaTeX.

Also included is BibDesk, LaTeXiT (a standalone equation editor that includes PDF drag-n-drop to Keynote and other such programs), and Excalibur (spell checker that can work with TeX code).

2. For a more WYSIWYG interface, there's LyX. The output isn't perfectly WYSIWYG, but it's definitely good enough that you don't have to preview very often. I believe it used to require X-windows, but no longer does, which is nice.

It also has other nice features, like Branches, which lets you tag material for optional inclusion in the final document. For example, create an exam by creating the answer key that includes both questions and (in-place) answers. Mark the answers as being in the Answer branch and you can include or exclude all of them in one step.

It also supports change tracking as many wordprocessors have: deleted text shows as strike-through, added text as blue, etc. You can go through a changed document and accept/reject changes. Further, it also supports (RCS-based) versioning that might be useful in a very structured workflow or for group collaboration.

It even does a quite decent job of reading pre-existing LaTeX documents in. And if you find the right article on the web and follow the instructions, it has support for using R's Sweave, which is very, very sweet.

Comparing the two: TeXShop is the more traditional LaTeX tool, while LyX is more for the GUI age. LyX does not include an installation of TeX, so you have to obtain that separately. (I installed TexShop first, so it was all there then I decided to try LyX.) LyX adds several features beyond TeX (branches, etc). Either choice is good, though if you're more oriented to creating technical documents than to getting into the mechanisms by which you create technical documents, I'd say that LyX is a better choice.

(We really need to start a thread on Literate Reporting sometime. I've recently discovered R's Sweave and it's pretty cool. I can see why Literate Programming has never taken off, but Literate Reporting makes a LOT of sense and does not really require anything beyond what you'd do to analyze and make a report anyhow.)

other programs to add to list...

Hi,

I wold recommend http://www.graphsketcher.com/ because it is so easy to do a graph mock-up, to help designing yout plots.

For real data analysis graphics I use R (and the ggplot package), though I recently got JMP (Mac + Win) which looks pretty promising.

For finding and recalling I use zotero (FireFox plugin for making bibliographies) and TiddlyWiki (http://www.tiddlywiki.com) with tiddlysnip and Google bookmarks.
Locally I recently discovered yep (http://www.yepthat.com/ ) and it is brilliant. It finds and catalogs all those PDFs of papers very fast and lets you browse thumbnails of the covers (with a cool magnifier tool). And you can add tags as you wish.
I am also looking at leap, which is similar but for all files.

DaveG

MacPorts

This is a lifesaver for anyone coming from the Unix world. Macports (or Fink if you swing that way), bring just about all Unix tools you know and love to the tips of your fingers with ease, so you don't have to go compiling things yoursef, figuring out strange dependencies, or downloading separate mac-specific apps for simple command lines utilities.

www.macports.com

Additionally, VMWare/Parallels can be lifesavers if you need to run certain applications that don't support OSX.

3D plotting

The best 3D plotting software I have found for the Mac is DataTank. It is starting to get old ( I think the author is focused on DataPlot) and the help is disastrous, but the GUI is so much more nice and intuitive than others (Igor Pro, I'm looking at you) that it is totally worth it.

Editor's note: this comment has been updated by its author, please read the other comments below for further information

Regarding DataTank

I'm very surprised to hear that my help is considered disastrous. I certainly thought I was better than that, and always try to respond to people very quickly. An e-mail might fall through the cracks, and attachments can sometimes be caught by an overly aggressive spam checker, but hopefully not frequently. The discussion board that I set up is another way to communicate.

It is true that DataGraph and the DataGraph framework are getting more attention from me these days than DataTank. I do address requests and bug reports for DataTank however, but I haven't reshuffled the UI recently or made large changes. The LaTeX type parser was however added to DataTank from DataGraph recently.

To sum up what I make
DataTank - focused on analyzing spatial data and algorithm development. Good for 2D, 3D
slicing and dicing and large data sets. Handles time series very well (for example from CFD computations)
DataGraph - Graphing, some standard statistics, but focused on being easy to use
quick, and create clean publication level results. It does scale fairly well, but not as much
as DataTank that uses a hybrid disk/memory approach.
dgraph - a command line utility to create graphs based on DataGraph files and text data files.
Get access to this once you register DataGraph.
DataGraph Framework - A cocoa framework that allows you to use the graphics engine from DataGraph in
your own Cocoa applications. Very quick to incorporate and is basically to graphs what
the Interface Builder is to user interfaces.

David

Clarificaction

David is right, and I want to apologize: I didn't mean his support help, but rather the help files included in the program. And even then I was wrong, since I didn't realize there has been a new version of that help for a while that I didn't know of. My comments pertained some old version of the help files, the new ones are great and so has always been DataTank's email support.
Seriously, I suggest people give it a try. I have tested almost all mac visualization programs (even expensive ones like TecPlot) and DataTank is superior and in a class of its own.

Visualization Shootout Article?

Would you be willing to write a "shootout" or comparison article for MacResearch. I think a lot of people would like to hear opinions on TecPlot vs. DataTank vs. ... I know my old review of Aabel was well-read.

For microscopy, TLC and gel image quantification

I think ImageJ is a very useful tool for those who need to enhance simple images like thin layer chromatograms or electrophoresis gels. It also could be used as a densitometry program. And (perhaps its primary function) it's a perfect software for confocal microscopy data analysis. It's written in Java, is cross-platform, and free.

The software I use (geochemistry)

Well, some of my favourites are already listed (LyX is a must...).... I like JabRef a lot. It's a kind of Papers but from the Bibtex point of view: you can create bibliographic databases importing cite researchs from the main bibligraphic databases and then you can export them to LaTex or LyX, but also you can use it to link to your pdf's. Is not as fancy as papers, but to me is very helpful...and, is Open Source!!!!

Besides LyX, I also use NeoOffice as most of the geological word is controlled by Word documents...

For 2D graphics: Kaleidagraph, Plot (free and powerful) and in the next future SciDavis, when I will be able to run it in a Mac.

Cheers,

Jordi

SPSS alternative

I always suggest JMP for statistics. My department is almost entirely devoted to SAS. Everyone here insists that the only way to do statistics correctly is with SAS by hand-coding from scratch every time.

JMP is from the same company, has a graphical interface, stores the data inside the same file with the analysis, and I've yet to find something I wanted to do in JMP that I couldn't figure out. Also, after taking the extra time the first try, all subsequent attempts take less time to do than screwing around trying to hand code the analysis.

P.S. I also suggest using Skim in conjunction with Papers. You can edit PDF's in Preview, but their are more options in Skim and is easier to use. (To prevent irrevocable edits, I save 2 copies of each article after editing. One is a PDF bundle (PDFD), and the other is as a regular PDF with imbedded notes)

Pretty much the same here

An example of software bundle from a geoscientist standpoint

USING WITH GLEE:
- OmniFocus for task management (sync to Palm using the MissingLink although swtiching soon to iPhone + omnifocus)
- GanntProject for project management -- Free and cross platform
- Papers for pdf library and references (switched from JabRef which is a reasonably good free and cross platform app).
- TexShop for LaTeX (sometimes use Texmaker for quick and easy visual debugging (colored text) or line numbers) --Free
- Pages for text processing
- Matlab for mathematical computing
- KomodoEdit (editor for programming) -- Free. TextWrangler or Smultron are another free options, more lightweight than Komodo.
- Fink for all *nix thingy (GMT, wget, rsync, etc) --Free
- Parallel Desktop (for my ONE software that requires Windows XP...).
- Quicksilver for quick access to applications, etc (faster than Spotlight) -- Free
- mucommander for some specific directory operations -- Free

TRYING AT THE MOMENT:
- OmniOutlinerPro for gathering research info, draft ideas, etc. So far so good (almost ready to buy it) but still hesitating with DevonThinkPro.
- OmniGrafflePro (almost ready to buy it). Presently using Inkscape (Free) but it took me 1/10th o the time to make the same illustration with OmnGraffle.
- Scrivener. Great but minor details still prevent me from buying it (When using Edit Scrivenings for several documents, I would like the documents' titles to appear in the next (e.g., Intro...) without manually adding them, which becomes a mess when exporting the doc).
- GraphClick: soon to be convinced!!

Stata and LaTeX

I see a lot of the applications that I use and depend on here, but one I've not seen listed for statistics is Stata. I used to use JMP (and SAS on PCs) and have tried almost everything I could get my hands on. What sold me on Stata is that, unlike SAS, they don't treat the Mac as a bastard child. That is, there is NO lag between the Mac and Windows (or other OS versions) in features, capabilities, etc. I just got sick and tired of having software that was behind the Windows version's capabilities.

Stata isn't cheap, but educators get substantial discounts. They have several versions of it with different capabilities, and unless one works with very, very large datasets, the less expensive versions are more than adequate (not 100% sure but the versions differ in their capabilities as to size of dataset and multiprocessor use). I save several hundred dollars by buying the 'basic' documentation. Basic is about 8 or 9 volumes of documentation, each at several hundred pages! Also, whenever I've had a question, I always get a response (complete with code!) within a day, and the same person will continue to work with you to make sure you have all that you need.

Moving on to LaTeX, I highly recommend downloading the MacTeX package and either using TeXShop or Lyx for writing. Although the learning curve is somewhat daunting,

You can get MacTex here: http://www.tug.org/mactex/

Another excellent tool for

Another excellent tool for volumetric visualisation is ParaView. Unlike DataTank it is free and open-source. Works nicely both on PPC and Intel machines. As the name of the program also suggests, having a multicore/multiprocessor systems helps greatly.

Dr Hüseyin Hacihabiboğlu
CDSPR, King's College London
http://www.hacihabiboglu.org

The Ideal software bundle for scientists... and grad students

I have been on the search for the perfect set of scientific software from the standpoint of a graduate student in solid state chemistry. Because I am a starving grad student I had to be very picky about what I purchased what is free/ open-source. Here is what I'm currently running.

Math and Stats
Mathematica
DataTank: Recent convert (about a week) but this is awesome and the developer is really helpful.

Plotting
Datagraph: Was my gateway drug to DataTank, I switched to Datagraph when it started to seem that Plot was no longer under active development (David added a support for importing Plot files for those of you still using it). Again the developer is really good about communication and is very willing to add functionality to the software. Well worth the money.

Data Analysis
fityk
CrystalMaker suite (site licensed)
Macnification

Writing and Research
TexShop
MacTeX
Jabref
Papers
Office 08 (Mostly for paper writing with my PI, but excel is handy every once in a while... I only have it because my PI gave me the funds.)

Project management
Things: come on... we scientists... we need another brain to keep track of the minutia... things is great.

My Stuff

This is what i use right now:

Literature:
- BibDesk
- Skim

Math/Plotting:
- ipython/numpy/scipy/matplotlib/pytables
- Igor Pro

ToDo List:
- iGTD

Text/Editing:
- TeXShop + TexLive
- BBedit
- VIM

Misc:
- sshfs
- OmniGraffle Pro
- XCode
- Mercurial or Bazaar as version control system (can't decide yet)
- Platypus makes nice dropable apps out of shel/python/whatever scripts
- VMD Molecular Graphics Viewer
- VMWare for virtual Linux installation for one of our lab software

That's all software I need right now and I am happy with it.

Re:My Stuff

I would like to second Skim. That program is amazing. Much better than Preview or the built in reader in Pages. For me, that is primarily because of a great full-screen reader and the ability to take scrollable snapshots of the paper so that you can look at the ToC or a figure while reading the text related to it.

OmniPlan

As a grad student working on strict deadlines and having to stay on tasks during huge periods of free time and prevent myself from procrastinating til the last minute but not work so much that I burn out, OmniPlan has helped me space out my tasks, complete with time estimates and amounts of times on specific days that I will work on them.

It is expensive ($90 for educational version) but it has been indispensible for me working on my PhD work. There is just too much free time for me to manage without it. I usually either work too much at the beginning or end and get burned out. This helps me space things out.

The Ideal Software Bundle for Scientists

My list is:

OmniFocus
OmniGraffle
Filemaker Pro
iWork, except PAges
Papers
Mathematica
Nisus Writer Pro
Mindmanager
Webstractor

I would drop Nisus in favour of Pages, giving better integration between all iWork programmes, if only I figure out how to insert a numbered caption under a table or graph in Pages. Does any one know ?

what about GNUPlot for plotting?

Our whole lab uses gnuplot for a lot of our plotting needs. Anyone else use it?

My software consists of Textmate with FORTRAN plugin, gitHUB for a repository (so using git and utilizing the TEXTMATE project drawer plugin). Then PAPERS for my article management and fianlly OmniFOCUS, with iphone app, to keep track of all I need to do.

From my perspective

(computational math)

* TextMate (coding, TeX:ing)
* gcc + mpicc
* MacPorts (invaluable)
* ParaView (Great visualization software)
* LaTeX (teTeX distribution)
* Beamer (for presentations)
* BibDesk (for reference management)
* Matlab (the Mac version is unfortunately subpar)
* Python (Scipy, numpy a little bit. Transitioning from matlab is cumbersome though)
* MacFuse + MacFusion (a neat way of managing remote directories)
* PsyncX (for backups)
* Mercurial (for revision control)
* Trac (Web based project management which runs on Mac, with wiki, etc. Interfaces with Mercurial via plugin)

All is free, except for TextMate (which is inexpensive) and Matlab.

thanks for such an important

thanks for such an important and useful info.

Adison High School

It sounds like you want to

It sounds like you want to hook multiple keyboards, mice and monitors to the mac Pro and then have each student work off of that. I doubt that can be done. But even if it could, I think there would be a performance penalty.