Matlab for Mac

There are changes to Matlab under Mac OS X. In particular, OS X "Lion" requires Matlab R2011A or later. Our group license servers will not be able to upgrade to a license key for R2011A, due to licensing changes from Mathworks.
Instead, users needing R2011A or later will need to point their Matlab to our new license server. We currently have this running on a temporary machine for testing and early deployment, but we need to defer rolling out R2011 to all of ECE until we've had time to build and test our new department-wide server (which will be virtualized, so we need to license and configure VMWare server, etc. as well.)
Current Mac users who want to upgrade to OS X "Lion" will need to contact us about getting R2011A or newer, set up to use the temporary license server.
We're distributing the Mac edition via USB key, as this is much simpler for users than running the installer.
(Editions of Mac OS earlier than "Lion" can still use Matlab R2010B or possibly even earlier, using the existing group license servers.)

Scientific graphing

Further to my earlier post on advanced graphing, here are a few more options.

Now and then students ask about getting SigmaPlot, Origin or similar high-end data analysis, plotting and graphing software. Unfortunately the main commercial products in this field are quite pricey. An academic license for SigmaPlot lists at US $549. Origin for one UofT PC costs $550. OriginLab does have much lower prices for Student Personal Use licenses, ($50/yr.), but you must pay with personal funds and the license can only be used on a student-owned computer (your own laptop or home PC, not an ECE PC.) OriginPro Student Personal Use license 

Fortunately, for any task as broadly required as this, we usually find a range of good, low- to no-cost software as well. Many may be less polished or have fewer features than the top commercial entries, but are well worth checking out first. Here are a few I've dug up so far:

The Licensed Software Office carries IBM SPSS, popular in the social sciences, for Windows, Mac and Linux at $80 for a one-year license (Aug.1-Jul.31) for Faculty and staff, or $60 per year (Oct.-Oct.) for students.

SciDAVis is free, open source software for 2D and 3D plots, available for Windows, Mac and Linux: SciDAVis feature summary.

The free statistical programming language called 'R'  has powerful graphing and plotting features, as I mentioned in my earlier post on advanced graphing. It is available for Windows, Mac and Linux.


QTiPlot is a lower-priced alternative to Origin, SigmaPlot, SPSS etc. It has a variety of licensing options and pricing.

DPlot for Windows costs $195 and offers a time-limited free trial (output images contain a watermark).

Matlab "clones"

Our department has a Matlab license with quite a comprehensive lineup of specialty toolboxes and Simulink blocksets. Students and staff are allowed to use this license remotely from anywhere within Canada, the USA and Mexico (why these? something to do with NAFTA, apparently.) So please don't use our ECE network license to run Matlab on a computer located outside this region (remote login from anywhere to run the code on one of our computers here is permitted.)

But what about after graduation, or for friends and family who may need powerful simulation, matrix arithmetic and m-code functions? Well, aside from the Student Edition of Matlab, there are a number of free products available that provide some similar functionality, including an effort at m-code compatibility. This page offers a write-up on three such packages: FreeMat, Octave and Scilab.

I've heard good things about Scilab in the past, though I haven't tested out any of these three. Prof. Mann has made extensive use of Octave, I understand.

Base windows config

The set of things we recommend for any Windows PC, and which we aim to keep installed and updated on PCs we manage, covers a range of free add ons. Here's a start at a current list, as of June 2011:

• Windows Update or Microsoft Update - all updates, patches and service packs
• A current commercial antivirus subscription
• Symantec Endpoint Protection is free to all UofT users at antivirus.utoronto.ca
• MS Security Essentials
• Mozilla Thunderbird email client - currently at v.3.0 from mozilla.com
• Web browsers (MSIE required; user choice of Firefox, Chrome or both)
• MS Internet Explorer browser - currently at v.8, with v.9 forthcoming
• Mozilla Firefox - currently at v.5.0, download from mozillamessaging.com/thunderbird/
• Google Chrome - currently at v.12.0 download from google.com/chrome/
• Spybot S&D anti-spyware - free from www.safer-networking.org - protects browsers
• uncheck "Use TeaTimer" during install
• update, then immunize (takes some time) after that it will auto-update periodically
• Browser plug-ins:
• Adobe Flash player from get.adobe.com/flashplayer - visit in each browser
• Web of Trust search security tool - visit www.mywot.com in each browser and click the button to add the corresponding plug-in for that browser - repeat for MSIE, FF, Chrome
• Adobe Reader X download from get.adobe.com/reader/
• Putty 0.6 - download from sgtatham - copy to All Users--Desktop
• WinSCP standalone - download from winscp.net - copy to All Users--Desktop 
• 7-Zip free archive reader/writer from www.7-zip.org - reads WinRAR format
• Mendeley citation manager application and browser plug-ins from www.mendeley.org
• optional addition: Zotero plug-in for Firefox from www.zotero.org
• Browser setup (in all chosen browsers)
• bookmarks/favorites for commonly used UofT sites (library, IEEE, ECE, group, etc.)
• Google Scholar preferences: add UofT as a library for "GetIt(TM)" links in results

GetIt(TM) at Utoronto in Google scholar search

There is a preference setting in the Google Scholar website to let you tell it what libraries you belong to, including the UofT library system.
Go in advanced settings, fill in university of Toronto as a library, and save settings. From now on, your search results in Google Scholar will be annotated with links to access full text of articles and books that our library has. The link says "GetIt(TM) at Utoronto"
Using this on campus gets automatic access to content held by our libraries. To use this from off campus, you need to use the library portal, myaccess.library.utoronto.ca and log in with your UTORid.

Advanced graphing

Several packages exist for graphing and plotting data. This is just a sampling of some options.

• Matlab's built-in charting via the plot() command is quite powerful; you need to read up on various options to get the most out of this feature. 
• Microsoft Excel has extensive charting and graphing features. Whole books have been written on these...
• Unix and MacOS users can use gnuplot and there is even a Windows implementation in cygwin.
• Dedicated statistics software such as SAS, SPSS and Stata have their own charting features. UofT's Licensed Software Office carries these three packages.
• A more expensive dedicating plotting software package is Origin/OriginPro from OriginLab. Educational pricing starts at $500, so this is a premium option if your supervisor's grant can handle it. See this page for Origin academic pricing and terms. They offer a low cost student personal use license at $50/year, 2 year limit, but only for use on student-owned PCs - you cannot use this on a PC owned by ECE/your supervisor.
• The open-source statistical programming language "R" for Windows, MacOS and unix/linux has graphing capabilities; see this intro to graphing in R
• Those coding applications for the web or for a desktop O/S have a number of options to incorporate data plotting:
• python programmers can use Matplotlib
• Javascript developers can use flot along with jquery, which I found very effective for my website's interactive scatterplot

One post on physicsforum also listed these other alternatives to gnuplot, which I haven't tried, but which look promising: 

• GRI, a language somewhat like LaTeX for coding scientific graphics (no GUI)
• Asymptote, a technical drawing vector-based graphics language
• Octave, a GNU project similar to Matlab
• GLE, Graphics Layout Engine, a graphics scripting language that uses LaTeX and supports mathematical formulas. The latest edition includes QGLE, a GUI editor for GLE objects.

MathType, or something else?

Engineers need to compose equations, often quite elaborate ones, for their publications and talks. There are a number of ways to do this, and we've seen people try and use many of these here in ECE:

• TeX / LaTeX - a free, open source package; a long-established text markup system, requiring a processor to convert from the marked up text to the formatted output.  Available on Linux and Solaris without any GUI, can generate PDF or PostScript output for printing; preview PostScript files with ghostscript. Several implementations also exist on MacOS and Windows. I'll cover LaTeX implementations in a separate post.
• MathType - a commercial product, an add-on to Microsoft Word. The built-in equation editor in Word is actually a simplified version of MathType. (Hint: try the MS equation editor first to see if it is adequate to what you need.) The commercial MathType package offers more symbols and equation layout types. You need a license for each PC on which MathType is used. We don't have a site license for this. Your supervisor can order single copies direct from the publisher, Design Science. Academic pricing is modest at just $57. A free 30-day trial is available (just don't try to do your whole thesis on the 30-day trial! If you need this, ask your supervisor and it should be possible to pay for a copy. If not, then check out the free alternatives in this post!)
• OpenOffice.org Math - For those running Open Office, the open source clone of MS Office, you have the option to install this free plug-in similar to MS Equation Editor. Beware that equations entered in this way may not display or output correctly if the document is opened in MS Office itself (i.e. in Word or PowerPoint.) Bring a copy of OpenOffice with you, or export to a PDF for presentation or print output, and verify the quality and accuracy of the results.
• One other I have not seen but that sounds worth checking out is MathCast, a free, open-source product for MS Windows. It supports both Word and OpenOffice.org Writer, and is built on open standards XHTML and MathML.

I learned about MathCast from this page on eHow: http://www.ehow.com/list_6370631_alternatives-mathtype.html

Extracting data from a printed graph

I was reading about someone trying to analyse a data series for which they had only a printed graph. They took the trouble to estimate by measurement each point in the data series, so they could build a new graph from the data. A commenter in the discussion thread pointed out that software exists to help automate this process. That sounded like a potentially useful tidbit to note for future reference, so here's the link (just the Wikipedia page on this type of software, but it links to several products for this and includes useful discussion on how to get good results)

http://en.wikipedia.org/wiki/Converting_scanned_graphs_to_data

CNRI - handy handle extension for DOIs in Firefox

If you do any research online, you'll recognize the DOI: handle for Digital Object Identifiers. These text strings are a globally unique and permanent reference to the digital form of a published work. Virtually all academic journal publishers with a web presence assign DOIs for each article in their journals.

Following the DOI on the web leads the reader to the web page where the article appears. The page it leads to typically displays the article abstract, with links to the full text of the article as HTML and/or PDF, possibly restricted to subscribers only, and offering non-subscribers a choice to pay-per-view for the single article (at sometimes jaw-dropping prices...)

OLD WAY

The "old way" to resolve a DOI that was not already formatted as an HTTP web link to the abstract page was this:

• select the DOI string and copy it to the clipboard
• open a browser and visit dx.doi.org
• paste in the DOI string and click to get the DOI resolved

That's not so hard, but it does require a trip to a specific site - either memorize and retype its URL, or make it a bookmark among your top picks. I'm finding space for such frequently needed bookmarks has gotten crowded over time.


NEW WAY

This handy Firefox plugin CNRI Handle Extension for Firefox lets Firefox users avoid the need to visit dx.doi.org, and simply paste a DOI: string into the address bar. The plug-in adds a new URI type "DOI:" that Firefox now understands. It does largely the same thing as visiting dx.doi.org and submitting the DOI string there, but saves a trip to that page. The resolving happens in the background.

After adding the plug-in and restarting Firefox, I tried this out and pasted "doi:10.1175/2010JCLI3500.1" into the address bar. It worked! The browser went directly to the J.Clim. page for this paper. It did not even rewrite the address bar to substitute the HTTP:// format URL for the same page. That's a point to beware of: if you start using this, remember that everyone else may not have installed it yet. If you want to post or link to accessible URLs for others to get to an article you're citing or assigning, be sure to find the "permalink" HTTP:// URL for the abstract page, rather than just the DOI string.