This is a guest post by Jeremy Sanders about the plotting package he’s developed. Jeremy is a postdoc working in the X-Ray Group at the Institute of Astronomy in the University of Cambridge in the UK.

Veusz (pronounced “views”) is a python-based GUI plotting package that I (Jeremy Sanders) have developed. As an astronomer, I was dissatisfied with every plotting package I had used. Some were fairly easy to use but old fashioned and/or limited (e.g., qdp, sm, grace, gnuplot). Several were not licensed freely (e.g., sm, idl). Many were difficult to use, requiring libraries of other peoples’ code or a lot of work going through manuals (e.g. idl). I wanted a free, easy to use and powerful package and so I started writing Veusz in 2004. Although I initially found the command line interface to be the most important part of a plotting package, since developing Veusz, I now use its GUI almost exclusively as it’s rather powerful and easy to use.

Veusz builds plots out of widgets, each of which has a set of properties and formatting options which can be modified. The standard way to build up the plot is to use the GUI to add widgets to form a tree, reading data from external files. However, most of the functionality can also be accessed using a command interface, which can be used from Python command line console window, an embedding Python module or commands sent to it from stdin. Indeed, Veusz saved documents are simply Python scripts using the same set of commands and are easily modified. Veusz can export several vector and bitmap formats, including PNG, EPS, PDF, SVG and EMF.

Veusz supports many types of graphs. Have a look at the page of examples. Veusz has scatter plots, with optional error bars (of several styles), joining-lines (stepped or beziers curves), fills and transparency, and allows for gaps in data. It also supports plotting functions (which can be defined using numpy functions or in external python modules), histograms (which can be computed from data), contour plots (including sub-contour levels and labelled contours), automatic data keys, image plots (with different color maps), color bars, shapes (including arrows) and external image files. It also has a function-fitting widget for doing a chi-squared fit to data. These plotting widgets are placed inside graph widgets. Multiple graph widgets can be placed on a page and in a grid widget which arranges the graphs inside it. Each graph can have as many axes as you like.

Veusz can read data in several different formats. It supports 1D numeric, date and text datasets, and 2D numerical arrays. Its default format is a simple space-delimited text format which can contain a descriptor describing dataset names, columns and data types, or specified in the program. It also supports CSV files (with an optional name for a dataset above each column). Importantly, it can load 1D and 2D data from FITS tables or images. And if that’s not good enough, you can send numpy arrays to Veusz using the embedding interface, or define an import plugin, which is a simple Python script for reading the data. A powerful feature is the ability to create new datasets in the program based on functions of other datasets. These datasets update automatically if the underlying data is reloaded.

Veusz is multiplatform as it is written in Python and uses PyQt for user interface and plotting. There are some small parts written in C and C++ to make the program faster. It relies heavily on the Python numpy libraries for handling data. Binaries are available for Linux x86, Mac OS X and Windows, and source allows it to be built for these and other platforms. It is licensed under the GPLv2.

Now, what it doesn’t do: It currently doesn’t have 3D surface plots or types of plots without independent axes at 90 degrees (e.g., pie chart, radar plot). The embedding interface doesn’t have a simple command for plotting like pylab, but it only takes a few lines of Python code to make a simple plot, and the object interface makes it very easy to manipulate the graph. Embedded plots can also be saved and loaded into the main GUI program for later editing. Its main feature which sets it apart is the unified command line interface which underlies the entire program. The program only supports Qt as a drawing backend, but this is easily extended to support other export files. For example the SVG and EMF export filters were written by me in Python. Veusz is also mostly a single-person software project, though I have included patches and ideas from other people.

What I’m currently working on is to add more general plugins allowing the user to add new dialog boxes to modify the plot and its data. I’m also going to add dataset plugins which would add the ability to define new ways to modify the data easily within the program without writing numpy expressions (e.g., FFT). I’ve just written code to improve the embedding interface allowing the user to treat the widgets in the document as Python objects (see the New style interface here). I’ve also added vector field plots and am looking into supporting new data formats (e.g., HDF).

The current version is 1.8. Please download and play with it! There are installation instructions, a manual, and a FAQ. Questions and comments are welcome below, on the mailing list, or directly to to me (jeremy at jeremysanders dot net).

Veusz (free), OS X [dmg] Windows [exe] Linux [tar.gz]

LaTeX, pronounced “la tech”, is a typesetting program that we use to write our papers (instead of Word or somesuch nonsense). Over the long US holiday weekend I got LaTeX and all of its bits installed on my new 13″ MacBook Pro (named Gloria). In this post, I’ll walk you through the installation and setup that should work for any of the code and text editors that Tom discussed a couple weeks ago (e.g., TextMate, TexShop, Emacs). In a future post, I’ll describe how to get TextMate setup as the primary LaTeX editor.

Read on for step-by-step instructions for installing LaTeX, AASTeX, MN2E, and more. One new thing that I learned was how to include both EPS and PDF figures in the same document!

Download and Install LaTeX

The easiest way to get LaTeX onto OS X is via MacTex. I recommend downloading the full package (~1.3 GB) and then customizing the install. The package comes with BibDesk, TexShop (which everybody seems to love except me), as well as lots of other stuff.

MacTex uses the paths.d method to modify the PATH environment variable. This works well if you don’t have your path explicitly set in the .cshrc/.tcshrc/.bashrc. To check if your path is set up correctly, in Terminal, typing which latex on the command line should return /usr/texbin/latex.

Download and Install AASTeX

AASTeX is the package for preparing astronomy publications for ApJ, AJ, and PASP. Download the AASTeX package and put it in ~/Library/texmf/tex/latex/aastex52. If you’re unfamiliar with AASTeX, a handy guide [PDF] comes included in the download. To use the AASTeX style, be sure this is the first line of the tex file:

\documentclass{aastex}

Setup emulateapj

If you want to get the fancy look of a two-column ApJ paper, you’ll want to use emulateapj. The MacTex-2009 package includes an old version so you’ll want to donwload the new one — emulateapj.cls — and put it in ~/Library/texmf/tex/latex/emulateapj.cls. When you want to use it instead of the AASTeX format, modify the tex preamble:

%\documentclass{aastex}
\documentclass{emulateapj}

Download and Install MN2E

MN2E is the package to use for submitting to MNRAS. Download mn2e.cls and put it in ~/Library/texmf/tex/latex/. Also get the guide [PDF]. To use the style file, make this the first line of the tex file:

\documentclass{mn2e}

Set up the Bibliography for Use with BibTeX

The easiest way to create the bibliography is with BibTeX and ADS. Your .bib file (managed with BibDesk or exported from Papers) should live in ~/Library/texmf/bibtex/bib/my_bib.bib. To get the bibliography to display in the journal style format, you’ll need bibliography style files (.bst).

The bibliography style file for use with with AASTeX is part of AstroNat. (However, be advised that many of the AstroNat resources are no longer necessary.) Download apj.bst and put it in ~/Library/texmf/bibtex/bst/apj.bst. In the preamble of the tex file, include:

\bibliographystyle{apj}

For MNRAS, download the bibliography style file, mn2e.bst, put it in ~/Library/texmf/bibtex/bst/mn2e.bst, and include this in the tex file:

\bibliographystyle{mn2e}

Where you want the reference list to appear (typically after the acknowledgements, before tables and figures), put this:

\bibliography{my_bib}

Figures

If you’re using pdftex instead of latex (as you should be…in this day and age, there’s no need for that DVI -> PS -> PDF rigamarole), you can include both EPS and PDF figures in the same document by loading these packages in the preamble of the tex file:

\usepackage{graphicx}
\usepackage{epstopdf}

The filename extension is optional. For example, to include pdf_fig.pdf and eps_fig.eps:

\begin{figure}
	\plotone{pdf_fig}
\end{figure}
 
\begin{figure}
	\plotone{eps_fig}
\end{figure}

Anything else? Once ya’ll give this the once over, I’ll go ahead and add it to the LaTeX wiki entry which is fairly outdated at the moment.

One of the things we spend the most time doing as astronomers is writing text and/or code, whether to develop a pipeline to reduce/plot data, write papers/proposals, or write simulation codes. Choosing a good text editor is just as important as having a good chair to sit on, and can have a big impact on productivity! In this post, I will go over a few of the best text/code editors out there for MacOS X.

If any text editor can be compared to a swiss army knife, it is TextMate. It provides support, through bundles, to over 150 programming languages (C/C++, Fortran, Python, Perl, Ruby, LaTeX, HTML, …) and tools (subversion, diff, mercurial, …). One can create projects with multiple files, search and replace text simultaneously in many files, and typeset LaTeX files. Customizable syntax highlighting makes writing text/code pleasant, and code collapsing and expanding makes editing long programs much more manageable (for example, one can ‘collapse’ if statements and do loops in Fortran). One great feature is the ability to just type ‘mate filename’ or ‘mate directory’ on the command-line, and have the file or directory open in TextMate. A number of bundles are installed by default to support programming languages, but if your favorite one is missing, there are instructions on installing bundles here. Be sure to check out the screencasts to make the most out of TextMate. At around $50, a license is a little pricey, but you can try out a 30-day demo to help you decide whether you like it! There is a 15% education discount, and larger discounts if you order 4 or more licenses.

Emacs needs no introduction, but what I want to mention here is not the old command-line emacs, nor the X11 version xemacs, nor the modified emacs for OSX, Aquamacs, but the official Emacs which is now available in native mode for MacOS X (no X11 needed). Emacs has support for many programming languages, and has fantastic auto-indent capabilities: despite being a heavy TextMate users, I always run Fortran 95 files through Emacs to tidy up the indentation! The Emacs team does not provide pre-built Mac versions, but cutting edge builds can be downloaded from this website. Emacs is, of course, free.

Another (free) powerful text editor that is definitely worth trying out is TextWrangler which is a ‘lite’ version of the commercial editor BBEdit. TextWrangler is simpler than TextMate, but has saved me in a few cases where strange non-ASCII characters have made it into a text file, as it has a nice ‘Zap Gremlins’ feature than can remove any non-ASCII character. Syntax highlighting is of course present, as well as the ability to open multiple files in the same window. One very useful feature is the ability to edit a file directly from an FTP or SFTP server (SFTP basically allows you to access files on any computer that is accessible through SSH).

Finally, no discussion of text/code editors would be complete without mentioning the unavoidable TexShop that many of us already use to write papers/proposals. It is a great LaTeX editor, but many users miss out on some very useful features. Some features that may have eluded users are: if you press the command (apple) key and click on a word in the source, it will show it in the PDF, and vice-versa; there are very useful LaTeX and Matrix windows in the ‘Window’ menu, that make it easy to insert mathematical/greek symbols, and build matrices, without having to lookup how to do this on the web; and there are many scripts to typeset a file, not just the default ‘Latex’: for example, the cryptically named ‘latexmk’ will actually run the usual latex/bibtex/latex/latex that BibTeX users are familiar with.

These are just a few of the text/code editors available on MacOS X, but we think that these are some of the best available. Do you use any of these? Do you know of any other great text/code editors?

TextMate, $50, $42.50 educational, bulk and site licenses
Emacs, free
TextWrangler, free
TexShop, free

While the Mac OS X provides us easy access to the much-beloved terminal, by itself, it is very limited. Apple does not support or maintain its Terminal or X11/XQuartz applications; it is rather supported by an independent group of developers (see XQuartz wiki). However, as the Mac OS X is built on X11, there is no need to install a complete UNIX OS, it does require quite a bit of work to make your machine Unix-capable. For long, the open-source project Fink has long been our savior. Over the past few years, MacPorts has developed as a very nice alternative to Fink in the last couple years. While both systems serve the same purpose, there are differences that make one or the other more appealing. For e.g., if you only need a handful of applications (and not the entire Red Hat system), MacPorts is much easier and faster to install. It takes a couple minutes, which is miniscule compared to the ~45 mins needed for Fink. The caveat being that while Fink installs most of the basic tools and libraries that will be needed in the future and ‘completely’ builds the Unix environment, MacPorts only creates the basic directory structure during installation. For this reason MacPorts uses less hard disk space as well. Of course, you can build ports from fink in MacPorts and vice versa — it just takes a little more effort. In my experience it also takes 3-4 attempts before you get Fink installation right.

The other (big) advantage of Macports is its more active developer base; hence, the various packages tend to get updated quicker. While it is not necessary to keep your packages updated by the day (or the month), it is always nice not to have to wait months for a fix. The good news is that the Macports port library is becoming as extensive as the fink library despite its late start. Again, if you have the expertise, you can always install fink packages in your Macports system as both are open source.

Pre-requisites: Assuming you have a Mac OS X, get the latest versions of X11 and XCode. That is basically it! Then go to the MacPorts install page, download the dmg, and start building any (or all) of its 7015 ports (in 92 different categories). And have fun!

Basic Commands: The average Macports user needs only a handful of commands to install, upgrade, and remove MacPorts. The MacPorts Guide talks about all of these commands (and more) in more detail. But this should be all you need if you are a basic user. You will need ’sudo’ for most of these commands, i.e., when write/execute permissions are needed. I have used ‘emacs’ as an example for package name.

update macports: port selfupdate
list all available (installed/outdated) ports: port list (installed/outdated)
search available ports: port search emacs
install ports: port install emacs
upgrade all (one) outdated ports: port upgrade outdated (emacs)
uninstall (deactivate) ports: port uninstall (deactivate) emacs
uninstall MacPorts: rm -rf /opt/local/ /Applications/MacPorts/ /Library/Tcl/macports1.0/ /Library/LaunchDaemns/org.macports.*

MacPorts PATH: Ports downloaded via MacPorts will be in ‘/opt/local/bin/’, separate from ports native to X11 (e.g. ls, cd, more, gzip, …) that are stored in ‘/usr/bin/’; MacPorts will automatically add this to your PATH on installation. Of course, if you download a port that already exists in ‘/usr/bin’, it will supersede the older one. No harm done, except for the few kilobytes in hard disk space.

Starting List of ports/apps: While the ports or apps you should download depends on your need, for the normal astronomer, I would recommend the following ports: aspell/ispell, teTeX, auctex, emacs/xemacs, gcc, ghostscript, ghostview, gsed, wget, rsync, tightvnc, perl, python, ruby, R, and gimp; see here for more info on these ports. When you install these ports, a lot more ports and libraries will be installed as dependencies, especially gimp will install a lot of ports. Of course, you should browse through the available ports page. Note that installing these ports will take a while (especially gimp) and might test your patience as each application is built from its source code.

Some GUI applications like the Chicken of the VNC, TeXShop, LaTeXiT, and Adium are also available via Macports. Whether you download the GUI by itself or as a port (will be installed in ‘/Applications/Macports/’), the functioning will be the same.

(Based mostly on the Macports guide, wiki, and FAQ).

JSkyCalc is an easy-to-install ephemeris tool that helps you plan your observing runs, then carry them out as efficiently as possible.  It’s a graphical revival of the venerable Skycalc by John Thorstensen of Dartmouth.

Airmass-plotting tools exist for ESO and Keck.  The advantage of JSkyCalc is that it calculates everything you’ll need for observing, and it knows all major observatories—one tool can plan all your runs.

There are 2 versions of JSkyCalc:  a web version, and a downloadable version.  I recommend downloading it, so that you can load lists of targets.  On my Mac (OS X 10.5),  a simple double-click of “JSkyCalc.jar” starts the program.

Here’s a simple demo.  Start JSkyCalc and select an observatory.  The main screen looks like this:

Enter a date & time (there’s a button for “now”).  Hit “Nightly Almanac” to see the times of sunset, sunrise, and twilight.  Hit “Object Lists” and load a set of objects; in this example I’ve loaded three standard stars.   (Hit “Help” to learn the catalog format.)

Select all targets with shift-click.  The “Sky Display” window shows you the positions of your objects with respect to the constellations and the moon.

At the telescope, hit “Set to Now” to show current conditions.  Even better, you can ask JSkyCalc to update in real time: try setting “sleep” to ~60 s, and hit “Auto Update.”   Select all targets, and check the airmass graph: a vertical bar shows you the current time.  This is a handy aid for deciding when to switch targets and observe standard stars.

That’s just a quick look.  JSkyCalc’s “Help” button has more details.

Two grumbles so far:  First, I can’t figure out how to PRINT!  I’m currently screen grabbing the airmass plot, and using “convert -negate” to make a printer-friendly version.  Anyone know a better way?  Second, since Keck has unique pointing constraints, you still need to use their tool to calculate how far down in elevation you can follow a given source.

JSkyCalc, free

(To those who noticed, apologies for the premature publishing of this post earlier this week.)

This is Part 2 of two-part series on keeping multiple computers in sync. Part 1 was about using Dropbox to sync files and applications.

For about three months, I used Fruux to keep my iCal and Address Book in sync on three computers (and one iPhone). I ran into so many little problems and annoyances with Fruux, I gave in and bought a MobileMe subscription ($100/year). I’ve been using MobileMe for three weeks and have been extremely pleased. The bottom line is that Fruux works well enough if you can tolerate duplicates and conflicts, but if you can afford it, MobileMe is a better choice. Read on for the gory details.

DISCLAIMER: I don’t fully understand the inner workings of all this…I figured out what works for me by trial and error. Proceed with extreme caution. Back up! Export Address Book and iCal Archives. Before syncing for the first time, I highly recommend googling your particular situation so you know what to expect. Ideally, start with a blank slate on all secondary computers: no contacts in Address Book and only one calendar in iCal. If you have issues, consider resetting sync services.. If that doesn’t help, try advanced troubleshooting. If none of that works, don’t ask me, contact apple or fruux or post in a relevant forum.

Fruux

Fruux is a free service that offers synchronization of many of the same things as MobileMe: Address Book, Calendars, Tasks, and Bookmarks; over-the-air syncing to an iPhone and a web app are in development. Fruux does actually work pretty well but it has some features that can be a little annoying. If you’re not OCD and can handle some imperfections in your Address Book and iCal, than Fruux is an economical and very functional option.

Problems that I had:

• Frequent syncing taxing the limited RAM resources of my MacBook Air.
• Frequent conflicts requiring my attention. Contact pictures, in particular, seemed to cause problems.
• Duplication of contacts and groups.
• Two versions of modified events. For example, 3pm meeting moved to 3:30 shows up at both times.

Advantages:

• Free

The workflow I settled on when using Fruux was keeping my primary computer “Always in Sync” and to only sync secondary computers when I was actually going to use them to schedule or to add or modify a contact. The reason why I didn’t keep all the computers “Always in Sync” was mostly due to the resources used by syncing and the annoying conflict messages. Their might be solutions to these problems, but I didn’t find them.

MobileMe

When I broke down and bought a MobileMe subscription, it just worked on 2/3 computers and on my iPhone. I’m only interested in syncing Address Book and Calendars; I haven’t played with all the other features of the service such as iDisk. (This article doesn’t make me eager to switch from DropBox to iDisk.)

The problems I have are:

• Cannot sync Address Book on one computer due to “Inconsistent Data.” This should be fixable, I just haven’t worked it out yet.
• All calendars, not just selected ones, sync on all computers and display on iPhone. This is a well complained about feature that I hope will be resolved soon.

The reasons I pay for it:

• New events sync to iPhone without actually having to do a wired sync.
• No problems with mysterious conflicts.
• Syncing is fast and doesn’t take any resources. I don’t notice it.

I also sync Google Contacts with Address Book. In order to get this to work for me the method I used was: delete all Google Contacts, export Address Book to vCard, import the vCard to Google. With this method, I lost the groups in Address Book, but I got them in Google…no biggie.

How do you keep your multiple computers in sync? Anyone out there loving Fruux? or not happy with MobileMe?

This is another guest post by Sarah Kendrew (blog, Twitter) a postdoc in infrared astronomy at Leiden Observatory working on instrumentation for the European Extremely Large Telescope and the James Webb Space Telescope. She’s also contributed an article about Evernote.

Staying on top of the literature, even in a narrow field, is one of the biggest challenges we face in research today. Do you have an ever-growing pile of astro-ph papers on your desk you’ve meaning to read? Yeah, we all have that. In recent years a number of software packages and web applications have come on the market to help researchers organise their literature: Papers, Reference Manager, Jabref, and Zotero. Past AstroBetter posts have introduced Papers and discussed Papers vs. BibDesk. A recent addition that’s been getting good press lately is London-based Mendeley. Here I’d like to share my experience and thoughts about Mendeley as an astronomy tool.

At its simplest, Mendeley is a very handy piece of software to help organise and keep track of the papers you have on your hard drive. Via a desktop application you can create a literature library of papers which can sort, create collections, tag and make the papers searchable. The programme parses pdf files and automatically creates a record for each paper, straight from the pdf. This works really well for recent papers, but for those that are older than 5 years or so, you may need to edit some fields manually. On the upside, the programme is good at sensing it’s done a bad thing and will prompt you to verify the info when in doubt. One missing feature is the ability to parse postscript files, these have to be imported and edited manually too.

Mendeley can actually re-organise your mess of papers into an ordered directory structure, sorted according to whatever criterion you want – author, date, subject and so forth. Say, if you store your papers in C:/papers, you can tell Mendeley to “watch” that directory. Whenever you save a paper to that directory from e.g. ADS, Mendeley automatically pulls it into your library database. So you don’t have to manually create a record for each paper you save to your HD.

When I’m writing a paper, where having my literature in order is key, Mendeley really becomes most useful. There’s nothing worse than spending an hour trying to find a paper on my hard drive, only then to have forgotten what I wanted it for in the first place. I write my papers in LaTeX, as most of us do, and use BibTeX for easy referencing. In one of Mendeley’s latest upgrades, automatic BibTeX file creation for each individual collection was added. So my collection of papers on, say, star formation now has a BibTeX file connected to it that gets updated every time I add a paper to it. It’s fantastic! For those using MS Word (a necessary evil for us instrumentalists), there’s a nifty add-in for referencing and creating bibliographies.

We have only seen the tip of Mendeley’s iceberg and what it is all about. Mendeley tags itself as “Last.Fm for research”, a social networking site that gathers info on what scientists are reading and saying about literature. The uptake in the astronomy community isn’t really significant enough for the reading statistics to be meaningful yet, but the online presence has many advantages. Users’ libraries are connected to an online profile, and via the website they can connect to colleagues and friends, and discover what others are reading. This doesn’t mean that your contacts see your entire library – but you can share publications with them, and if you add your own publications to your profile they will be visible to your contacts. My whole library is synched to the website, including annotations – so even when I’m away from my own computer I can look up references. I can also add things to my library via the web, using a Mendeley bookmarklet or directly from Google Scholar, NASA ADS, or even astro-ph. That’s what those icons are for in the right sidebar – who knew? So I don’t need to have a desktop application running all the time to add papers to my library – next time I open it, it’ll get all the new stuff I added from my web profile.

One of my favourite features is the ability to create shared and public collections. Shared collections are for collaborations, everyone involved can contribute papers and annotate. I’ve actually not used shared collections yet myself but imagine them to be very useful if everyone in a group is willing. Public collections are, as the name suggests, entirely public. I recently created a public collection called Gravity, to accompany a blog post concerning a paper on a novel theory of gravity; in effect I created a reading list to illustrate what I was talking about, that I can add notes and comments to. Public collections have an RSS feed, so anyone can actually subscribe to a collection and stay up to date with what gets added. They’re also embeddable, so I can add them to a webpage. For those of us who teach, this could be a really awesome way of connecting with students, providing them with supplementary material in a very low-effort way.

I haven’t sampled all of Mendeley’s features but for me it’s proven to be a great tool to help me stay organised. I used to stress about sorting out my hard drive to organise my papers, which were nicely ordered during my PhD but are now a total mess. Now I let this piece of software do it all for me. The one thing it won’t do is send the information from the paper into your brain. There’s no app for that, only grad students/postdocs (delete as appropriate), so hang on to those for now.

Sarah Kendrew blogs about astronomy science and politics at SarahAskew (RSS, Twitter). She is also a postdoc in infrared astronomy at Leiden Observatory working on instrumentation for the European Extremely Large Telescope and the James Webb Space Telescope.

This is a guest post by Sarah Kendrew (blog, Twitter) a postdoc in infrared astronomy at Leiden Observatory working on instrumentation for the European Extremely Large Telescope and the James Webb Space Telescope.

The tag line of note-taking application Evernote reads “Remember Everything”. The great thing is, with Evernote, you don’t need to remember. If you make it work for you, it’s like carrying your brain around on your laptop or phone.

I started using Evernote about a year ago and it’s quickly become one of the most-used applications on my laptop. I should mention that nothing it does is particularly astronomy-related—but as a general productivity app it does an excellent job for me. So how does it work? The concept of Evernote is simple: it’s software you use to create notes—about anything and everything you like. A note can be typed text, free-drawn (an “ink note”), a picture, a website, an email, a voice note, a tweet or any combination of the above. You can access and create notes on three different fronts: the web, your desktop (Windows and Mac, no Linux app yet), and your mobile device (iPhone, Android, Blackberry, etc.). I love it because it simply works, it’s versatile and easy to use, and looks good. Read on to learn more about Evernote.

I’m an instrumentalist working on large international projects, and that means I spend many of my days in meetings (or travelling to them) and telecons, all of which require some note-taking. I used to do this on paper but I don’t like cluttering my research notebooks with random meeting notes—and having separate notebooks for meetings is too much stuff to carry around. I’ve set up notebooks in Evernote for each of my projects, and I create notes whenever I need to write something down in a meeting. Notes can be tagged, geotagged and are date-stamped, which makes them easy to retrieve at a later date. If I need to share my notes with the rest of the team, I can simply email the note directly to my collaborators.

Evernote for me is also an extension for my to-do list programme. While it doesn’t offer that much organising fuctionality, I use it to provide extra detail to my to-do tasks which I organise using web application Remember The Milk (RTM). RTM is a very nifty and flexible little app but it doesn’t support long nested multi-stage tasks. So in RTM I might simply list “update model by Jan 15″, and add a link to an Evernote, where I make a checklist of more detailed steps (tag: todo, sensitivity) or provide more information.

My favourite feature in the iPhone app is that a number of notes can be marked as Favourites, which stores them locally on your iPhone for offline access—fantastically useful when I’m travelling. Did you see a cool conference poster that you want to follow up? Snap a picture and dump it into a photo note. The iPhone app used to be a little buggy but recent updates have improved things a lot (and it’s free!). Using the web clipper, you can clip entire webpages or screenshots into a note, with a link back to the original site. This is great for, say, saving papers on astro-ph that you don’t have time to read at that moment (tag: astroph, todo), or for jobs you want to apply for (tag: jobs, harvard). Or record Christmas present ideas (tag: presents, christmas, mum).

The things I’ve mentioned here are just the very basic functions of Evernote, which has become very powerful with its latest updates. You can now attach files to notes and share notebooks with others. Signing up for a premium account increases your upload allowance from 40 to 500 MB per month, and gives added functionality such as searching pdf files and shared editing of notes. There’s also an API and there are tons of ways in which you could integrate Evernote into your daily tasks (e.g. output from models or other applications could be put straight into a note).

I wrote this post in Evernote. Obviously. I also created a shared public notebook containing this blog post and a number of screenshots illustrating its many uses, go check it out.

Have you found more productive ways to use Evernote, developed cool scripts, or have novel ideas of putting this great application to use? Leave us a comment.

Evernote, free

MarcoPolo is a very cool (free) application for MacOS X that uses information about the current state of your computer, or evidence, to automatically perform actions.

For example, one can use MarcoPolo to automatically change the Network Location if an ethernet cable is plugged in or a specific Wi-Fi network is present (useful if you need a different network location at home and at the office), automatically open up an application if a USB device is plugged in, or shut down certain applications and mute the computer if a projector is plugged in (useful if you want to avoid that embarrassing IM message in the middle of a talk).

MarcoPolo can use many different sources of evidence:

• Attached Audio Output devices (headphones/internal speakers)
• Discoverable Bluetooth devices
• Advertised Bonjour (Zeroconf) services
• Attached FireWire devices
• Assigned IP addresses
• Ambient Light level
• Attached Monitors
• Active Network Links
• Power source (power adapter/battery)
• Running Applications
• Current Time Of Day
• Attached USB devices
• Visible WiFi networks

and can perform the following actions:

• Set your default printer
• Change your desktop background
• Enable or disable particular firewall rules
• Set iChat status message
• Set the default IMAP or SMTP server for Mail.app
• Mount network shares (smb://, afp://, etc.)
• Mute or Unmute system audio
• Change OS X network location
• Open a file (an application, a document, etc.)
• Quit an application
• Enable or disable screen saver password
• Start/stop screen saver
• Change screen saver idle timeout
• Run a shell script
• Turn on or off Bluetooth
• Turn on or off WiFi (AirPort)
• Establish or disconnect VPN

that can be grouped into contexts, such as Work or Home.

But the key strength of MarcoPolo, which makes all this a lot of fun, is that you can assign different probabilities to different sources of evidence. So for example, you can use a specific level of lighting as a 60% chance that you are at home, and the fact that an ethernet cable is plugged in as an 80% chance that you are at work. All the weighted sources of evidence are added up, and the final context is automatically chosen!

Have you used MarcoPolo before? If so, what cool uses have you found for it? And if you are a Linux or Windows user, have you found an equivalent application?

Google Wave is a promising platform for online collaborations. It’s currently in a alpha/beta state and its growing pains are evident: slow and lack of notifications. I have been using Wave for two months and think it’s a great tool despite the drawbacks. It has proven to be incredibly useful for large scale collaborations where there are +10 collaborators.

The slowness and lack of notifications does leave a sour aftertaste sometimes. The slowness will most likely be rectified by the Google developers. But, users have taken on the notification issue into their own hands and we’re seeing multiple programs and plug-ins popping up. Below is a list of the Wave notifiers available for Mac.

Waveboard

The latest Mac Waveboard application was released on November 24th, 2009. Waveboard is under active development and it looks great. This is ideal for users who would prefer having Wave act as an application vs. a tab in your web browser. The user is notified of an update via the task bar and growl.

Unofficial-Google-Wave-Notifier

This creatively named application functions similarly to the Google Notifier application. It’s under development, so there’s a chance of running into bugs. For the sake of simplicity, this may be the most favorable option. The application shows updates via the task bar and Growl.

Firefox

There’s an experimental Firefox plug-in. It has 4/5 stars and +30k downloads and the users seem pretty happy with it. Wave updates are displayed in Firefox’s statusbar.

Chromium (Chrome Dev)

Alas, Chrome has finally been released for Mac! The only issue now is that its extension option is turned off. There is a way around it for the adventurous ones. Go and download the latest Mac Chromium build (the active development version of Chrome). With Chromium, extensions are possible. Once you have a recent build of Chromium head over to the Google Chrome Extensions site and install the Google Wave Notifier. This extension will notify users of updates in the Chromium menu region.

If you don’t have a Google Wave account and would like one, I have 15 invites to hand out on a first-come, first-served basis. Contact me at this link, temporary contact for anti-spam efforts, with your email address so I can send the Google Wave invite.