For my research I’m recently doing a lot of graph and network analysis. So far the tools in ESRI ArcGIS have been sufficient for what I was trying to achieve. I used their Network Analyst Extension and also the Urban Network Analysis toolbox by the City Form Lab at the MIT/SUTD for a more scientific application: the calculation of centrality measures. While these warrant some more in-depth articles in themselves, here I’d like to put a more technical focus on a really annoying problem when using Gephi on a more recent MacOS X system.
Gephi is an open source graph visualization and analysis software. They themselves describe it as follows:
Gephi is a tool for people that have to explore and understand graphs. Like Photoshop but for data, the user interacts with the representation, manipulate the structures, shapes and colors to reveal hidden properties. The goal is to help data analysts to make hypothesis, intuitively discover patterns, isolate structure singularities or faults during data sourcing. It is a complementary tool to traditional statistics, as visual thinking with interactive interfaces is now recognized to facilitate reasoning. This is a software for Exploratory Data Analysis, a paradigm appeared in the Visual Analytics field of research.
PC, Mac OS X, Linux, iOS, Android, Web 2014 Choice of Robots: Kevin Gold Adam Strong-Morse 300,000 PC, Mac OS X, Linux, iOS, Android, Web 2014 The Last Monster Master: Ben Serviss Jason Stevan Hill 250,000 PC, Mac OS X, Linux, iOS, Android, Web 2015 The Hero of Kendrickstone: Paul Wang Jason Stevan Hill 240,000 PC, Mac OS X, Linux, iOS, Android. Sergi on April 17, 2012 at 5:29 am. We are thinking about doing a Mac OS app too, also free. I hope you try it, it could be great if you can provide.
(Gephi website)
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It’s a Java-based application and hence available for a number of platforms, including Windows, MacOS and Linux. Now, this should make MacOS X users already listen up, since the story of Java on MacOS X has not been an easy one over the past few months year or so. Basically Apple deemed the official (i.e. Oracle) releases of Java 6 insecure and therefore started to publish their own. With the release of Java 7 Oracle stopped publishing Java 6 for the MacOS X platform completely. This sounds like a good thing, and it definitely is in terms of security. Nowadays MacOS X has complete control over the Java installed and running on more recent MacOS X systems. I think this is true for everything from 10.6 Snow Leopard, but may be wrong here, but definitely from 10.7 Lion and upwards (10.8 Mountain Lion and also 10.9 Mavericks).
The problems start when you try to run a Java-based application that requires Java 6 on one of these machines. Basically using such software doesn’t sound like a good idea, but in the case of Gephi there’s no way around it: it’s developed by a non-profit organization (the Gephi Consortium) and therefore doesn’t really have the means (in monetary terms) or the manpower to keep up with this kind of fast-moving developments. I don’t blame them! The interesting thing is that this poses quite a problem, since Gephi in its latest release 0.8.2 is not able to run on those MacOS X systems with Java 7 installed. (Interesting side note: when I tried to install the very same Gephi 0.8.2-beta release on my Windows 7 virtual machine it ran perfectly fine with the Java 7 installed there…) Since I’m working with quite extensive network graphs in my research I really wanted to have Gephi run natively (well, kind of, since it’s still Java…) on my Mac for memory reasons. So I scoured the web and numerous web forums for a solution to this problem. Two things quickly became obviuos: 1) I’m not the only one with this problem, and 2) the solution is actually quite simple but I only found it hidden deeply in a thread on the Gephi GitHub page. So to make things easier for fellow sufferers I decided to quickly put together a write-up of my experience. Spoiler alert: I solved the issue in the end!
I started unprejudiced with downloading said gephi-0.8.2-beta release for MacOS X from the official Gephi website: https://gephi.org/users/download/
It’s a 42 MB .dmg file that contains the Gephi application. The installation is therefore simple: just drag the .app file into the Applications folder on your Mac and you’re done. Or so I thought.
When I first fired up Gephi everything seemed to be fine. After a splash screen the main program window opened:
I selected the Les Miserables.gexf file to open, and confirmed the Import Report, after setting the graph type to “directed” (I found this information in the Gephi Quick Start Tutorial):
Gephi 0.8.2 Import Report
This was the result:
Gephi 0.8.2-beta empty Graph window on MacOS X 10.8.5
The graph window in the center of the application stayed empty. In addition, what you can’t see from the screenshot, I also got the blue beachball when my mouse crossed the (empty) graph window and the application was generally unresponsive. It even refused to shutdown when quit by ⌘Q. This last fact and some early search results directed me into the right direction: we’re dealing with a Java-related issue.
Basically, what most forum posts recommended was to install an old Java 6 JDK and be done. Yet, that’s easier said than done. As I mentioned above, Oracle stopped providing Java 6 for MacOS on their download page. Most commenters therefore pointed at the old Apple Software Updates for Java 6. It took me quite a while to find one that solved my problem by actually installing a Java 6 JDK onto my system. As recommended on some sites I tried the Java for OS X 2012-005 update, but to no avail. After an afternoon of cursing and digging deeper into the topic I finally found what I was looking for on the Apple Developer Platform: the Java for OS X 2012-006 Developer Package:
Please note that in order to access the Apple Developer Platform you need to login using just a valid Apple ID – no developer account necessary!
This will download a 158.1 MB image file called javadeveloper_for_os_x_2012006__11m3909.dmg onto your system which in turn contains a software package called JavaDeveloper.pkg. After installing this, I finally found a Java 6 JDK on my system!
You can check the installed Java Virtual Machines by looking into the folder /Library/Java/JavaVirtualMachines. Before this installation all that was in there was the most recent Java 7 JDK in a folder jdk1.7.0_45.jdk. (Yes, it’s a folder, even though it’s ending in what seems like a file extension .jdk) Now I was happy to see a new 1.6.0_37-b06-434.jdk in there, too!
Stay with me, we’re almost there!
All that’s left to do now is to tell Gephi to actually use this Java 6 JDK. While in a terminal window you can (and should!) make sure that your system still regards Java 7 as the currently active JDK by running the following command:
So here everything is alright, MacOS X ignores the newly installed Java 6 JDK and continues to go to Java 7 (1.7.0_45) for all its Java needs. Instead, Gephi needs a pointer as to where it can find Java 6. This can be done by editing the file gephi.conf. It’s living inside the Gephi application package and can be accessed in one of two ways:
MacOS X Finder: Open Package Contents
After right-clicking the Gephi application in your Applications folder in a Finder window, select the option “Show Package Contents”. Then navigate to the subfolder Contents > Resources > gephi > etc. Alternatively you can use the Finder tool “Go To Folder…” from the “Go” menu (or press ⌘⇧G) and enter /Applications/Gephi.app/Contents/Resources/gephi/etc. In there you find the file we’re looking for, which can be opened in any text editor. It should look like this:
The relevant part is the second-to-last section (lines 10-11) about the JDK/JRE locations. Here you need to uncomment (i.e. remove the leading # from) the second line and change the contents of the variable jdkhome to match the actual location of the newly installed Java 6 JDK on your system. In my case it looks like this:
Notice that it is not sufficient to enter the path to the aforementioned ...jdk folder, but instead you have to actually reference the subfolder Contents/Home/! Should you fail to do so you will notice that Gephi won’t start up anymore without any comment or error message. I have to admit that it took me a while to figure this out. The forum post that pointed me into this direction can be found here.
And now we’re done! After installing a Java 6 JDK onto MacOS X 10.8.5 Mountain Lion and pointing Gephi 0.8.2-beta to it, we can actually fire up Gephi and start using it! I hope this quick walkthrough can help at least a few lost souls – just let me know in the comments if you ran into any additional issues.
[Note – this article about a Gratitude Journal was originally written back in 2012, and has been updated several times to keep it relevant and timely!]
In the past, I have discussed why I think keeping a Gratitude Journal is an awesome thing to do. And, it is time to talk about it once again! After all, when something works well, you want to tell people about it! The best part about it is that it fits ANY budget! You can start off not costing anything!
I have been keeping a Gratitude Journal for some time now. Even though it has been in different forms, I have found that I feel empty when I am not using one. Have you ever kept one? While I am asking questions, do you know what one is?
What is a Gratitude Journal?
Anything can pretty much be a Gratitude Journal – an old notebook, a loose-leaf folder, a dedicated journal notebook, an electronic document, or even a collection of scraps of papers! There is no right answer to that it physically is – whatever works best for you and your lifestyle is what you should use.
Now that you have an idea of what it is physically, let me tell you what it REALLY is. A gratitude journal will become one of your most treasured items you possess! Within your journal, you will be writing down all the things for which you are grateful.
Your journaling can be something that is structured, such as writing down all the things for which you are grateful that occurred in the day; this writing can be the last thing you do before going to sleep. Or, as something comes into your mind, you can simply write it down. You can take time to write down as many things as you think at one sitting, or simply as they come into your thoughts. Your Gratitude Journal should always be readily accessible so when the inspiration hits you, you have the ability to capture the thought!
As you interact during the day, think about what you can journal about – this will often put you in a more gratitude-filled mood. When you are searching for gratitude, you will easily find it. When you spot something, write it down. You can date each entry or just keep it free-flowing. If you want to personalize it, you can include pictures you have taken to help immortalize the moment.
If you ever feel like you have had a miserable day and nothing seems to be going your way, simply open up your Gratitude Journal and start to read what you have written. After reading a few things, your mood and spirit will shift 180 degrees and help put you back into having an Attitude of Gratitude.
If you are skeptical about doing this, try it out for 21 days. Start with a notebook and date each page, starting with today. Commit to writing something for each day. After 21 days, look to see how you are feeling. You will see that by just journaling each day, you will feel like a new person.
Resources:
Things I have used for my Gratitude Journal:
• Simple spiral notebook
• Loose-leaf binder
• A nice leather binder with exchangeable filler pages (currently in use)
• I have created a document using Google Docs (http://www.google.com/docs) – this was accessible to me no matter where I am (as long as I have an internet connection)
• If you are into electronic solutions, you can use Evernote
• There is an iPhone app – Gratitude Journal
• For my Mac Desktop, I have used Journler (http://journler.com/)
Be Well.
Paul.
No Hope (sergi Collado) Mac Os Catalina
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