Scrivener, a great writing environment!

Writing about web page http://drhariri.com/blog/1384/scrivener/

Note: this is a summary of a blog post I wrote on my Arabic research blog (برنامج الكتابة الرائع Scrivener), a blog that I have been running for over 3 years, aiming to spread knowledge and resources to help postgraduate students and researchers in the middle east.

For a while, I have been finding it more and more difficult to use Microsoft Word for writing, especially when it comes to bigger documents.

I often find myself thinking about where to write a certain chunk of text and even if I decided, it is sometimes hard to quickly reach the section that I want to update/edit.

A couple of week ago, Paul, my supervisor, started a discussion with me on how best to store and work on my thesis. He suggested that I use a feature that exists in MS Word where documents can be linked together to a certain master document. So, I went ahead and decided to learn about this feature which I have never heard of before. However, while writing, it came to my attention that some users reported their files and projects becoming coprrupted as a result of using this feature. So, I decided that using it is too risky, so here is an X for that.

I decided to look for alternatives, and all of a sudden, I remembered a certain software called Scrivener, which seemed very inetresting to me about a year ago so I decided to follow their Twitter account back then.

I decided to visit their website and I found out that they have already released a Windows version as it only had a Mac version back then and although I use a Mac mainly, I didn't start using it back then.

I took a look at the introduction video and their website and it was fascinating to me to find out that many novelists, authors, journalists and even researchers have been using Scrivener and have been very happy with it.

I also started googling Scrivener and found that others are using it in education and research.

The main concept behind Scrivener is that it offers a great writing environment where documents are split into chunks of texts. Those chunks could be chapters, sections, a few paragraphs or a few lines. The beauty however about Scrivener is that if you decided to combine all of those chunks into a single document for printing or sending, this can be done automatically and very easily using Scrivner's compile feature.

What this means is, if you are writing and do not want to worry about structuring or stylying at all, you can do that without any problems, and once you finish you can tell Scrivener to combined everything and format it in a way you specify. So, you could tell it to format chunk's titles as H3, for instance and to format any higher level groups as H2s or H1s.

The big advantage in this case of course is, your writing space is always there and you are free to add as many chunks of texts or images as you want.

Scrivener of course is more than just a writing environment, it has many geat features that I suggest you check.

Inregration with Reference Management Software

Since its important to me to have the ability to insert citations within Scrivener as I currently do in MS Word, as it has my Mendeley's plugin installed, I decided to look for possible ways of integration. to my surprise, there was no way to do this with Mendeley at the moment. However, it seems that those using Endnote or Zotero have a better luck as both of those reference management software offer an RTF scan feature that can be used to update citations and references list once the final document is made.

This is a quick video showing how Endnote can be used with Scrivener:

And here is the longer version of it where the author, a PhD student, explains how he uses tools like Evernote and Scrivener in his research activities.

Any hope for those using Mendeley?

Well, personally, I wouldn't turn down a potentialy beneficial software just because it doesn't work nice with another one. In this case, I decided to use Scrivener and insert citations manually like I usually do anyway. However to stay alerted to where they are I write them, for instance something like (John, 2000), then, I highlight them in Scrivener.

I don't see a huge problem of not being able to automatically use Mendeley within Scrivener. However, I decided to tweet those @Mendeley_com and @ScrivenerApp to see if there are any chances for an integration between those 2 to be born, and to my joy! they said that they have met and they are working on something that will make it possible for Scrivener and Mendeley to play nice with each other! So, let's hope that they develop something for us very soon!

Join the campaign and spread the tweets for a Mendeley Scrivener integration!

By the way, if you use Mendeley and would love to use Scrivener, don't be shy to do just what I did, LET THEM KNOW!. go ahead and tweet to both of those great companies how you love to see an integration as soon as possible.

If you are new to twitter, use something like:

Hi! I'm very interested in an integration between @Mendeley_com & @ScrivenerApp please!

AbdulRahman Hariri : 22 Mar 2012 17:50 |  Tags: Scrivener Thesis Video Writing |  Comments (4) |  Close comments |  Report a problem

Atlas.Ti 6 vs NVivo 9: A Comparison

Follow-up to Potential uses of CAQDA software packages from A.Hariri's

A couple of days ago I received an e-mail from one of my research blog (in Arabic) followers asking for my opinion on choosing NVivo or Atlas.Ti. I've sent her a summary of some of the issues that I faced when I tried both of them.

Today, I was asked by a friend of mine, Salma Patel of why I chose Atlas.Ti over NVivo as well, therefore, I decided to write a detailed post about this to help those who may be looking into this as well.

I found that Atlas.Ti 6 and NVivo 9 were two of the most used software packages out there. So, I went ahead to do some research and I decided to try them both. I ended up choosing Atlas.Ti although I was much inclined to use Nvivo for the following reasons:

These are what I think some of the key issues I based my comparison on, when it comes to features, both software packages offer very similar set of features.

After writing this comparison, I have to say that I do not hate NVivo, I simply think it wasn't for me. Others may find working with NVivo is better for their own reasons. I still follow the development of both NVivo and Atlas.Ti, and I still retweet some of their announcements and so on to my Research Blog (in Arabic) followers.

I hope some of you out there find this helpfu! and I am happy to learn about your experiences with any of the mentioned software packages.

AbdulRahman Hariri : 01 Oct 2011 02:34 |  Tags: Analysis Assisted Atlasti Caqda Computer Data Nvivo Qualitative Software |  Comments (11) |  Close comments |  Report a problem

Potential uses of CAQDA software packages

About a year ago, I was looking into Computer assisted qualitative data analysis software (CAQDA) software packages that may help me in doing my literature review by allowing me to code certain passages within documents into codes that I could then easily explore or retrieve.

I think one of the potentials I saw in some CAQDA software packages is that if you code useful passages within lots of papers and documents into codes (which are similar to keywords), this will make it easier for you to retrieve those stored passages of texts within different documents.

For example: if I have read 100 PDFs and assigned things that I believe relevant to my research into codes, it would be much easier to just output the passages that belong to a certain code within those 100 PDFs in 3-5 pages (since other information within each document will be hidden) showing where every passage came from and how they can relate to each other (You can use relationships between them too!). This would surely be much easier than having to check all those 100 PDFs to try and find bits and pieces here and there that belong to the topic I am trying to write about.

Another potential where I personally think CAQDA could help is building a rich research library of journal papers and different documents over the years. Because, in many cases, a PhD might be the first step of your research career, especially if you are a lecturer or someone that is interested in publishing journal papers in the same field. I guess what I am trying to say is, lets assume that while doing your PhD you come across 100 journal papers that you consider important in your research field. After that, you become a lecturer at some university where you are expected to do more research. So you read more journal papers and you assign more information to codes within the CAQDA software. After a couple of years, you could have a very rich library of papers that you have already read and classified into certain codes or keywords.

After that, all you have to do really when you want to write a journal paper is ask the CAQDA to output information related to a keyword and start writing.

For instance, you may choose to first write a background, so, you output background information which you store in a code. Next, you may choose to become more specific, so, you may want to identify previous gaps and even gaps that may still be in need of research. You output information assigned to a code "Gaps in....." and you find all different arguments by different authors, etc...

I believe that using a CAQDA helps a lot when it comes to writing, if it was used by the researcher while he was doing his literature review.

I know that some would argue that it is not good to just read certain parts of the paper and assign them and just forget the rest of the paper may see like taking things out of context, but this is only true if the researcher himself didn't pay attention to that.

Of course I am only scratching the surface here as most CAQDA have much more advanced and useful features such as reports & networks diagrams where you could visually show the relationship between different passages. For instance, you could show a number of authors disagreeing with author A while may others are supporting him.

I have been working with a CAQDA software (Atlas.Ti) mainly as part of my literature review as I believe it keeps me organised and helps me find information that I have already looked into much faster than I would usually do. I will continue to use it as I go on with my PhD and I hope that I learn more about it and try the various features available and be able to share what I find or anything new later on.

AbdulRahman Hariri : 01 Oct 2011 01:50 |  Tags: Analysis Assisted Atlasti Caqda Computer Data Nvivo Qualitative Software |  Comments (0) |  Close comments |  Trackbacks (1) |  Report a problem

Wordpress Mac Permissions Issues with Zend Server CE

If you have installed Zend Server CE on your computer to use as a development server, you may have ran into the issue of Automatic update not working on Wordpress. This is the function that usually updates your Wordpress plugins and Wordpress system or core files. Furthermore, another related problem that you will likely to have as a result of this is that you won't be able to have Wordpress edit your .htaccess to change the way your blog URLS look like.

The cause of this problem is that the Apache user used by Zend Server CE (User: daemon, Group: daemon) is not given enough permissions to be able to make changes to your files on your Mac. The solution to this should be simple, at least it worked for me right away.

The Solution:

• Open your Terminal application (Applications -> Utilities)
• Use the following commands in bold:
  

1. Navigate to your htdocs folder that was created by Zend Server CE using something like:
   cd /usr/local/zend/apache2/htdocs
2. Change the user of your blog folder which resides within the htdocs folder. In my case my blog folder is called blog, so I used this command:
   sudo chown -R daemon blog
3. Change the permissions of the folder using:
   sudo chmod -R g+w blog

• Now, try to update your Wordpress plugins or Wordpress system itself (core files), this should have solved your Wordpress Mac permission issues. In my case, I didn't restart and it worked. If it doesn't work rightaway on your development environment, try restarting your Mac.

Note: The solution above worked for me because I don't allow any network access to my development environment, if you for some reason need better security, you should probably check Zend Server's documentation to follow their suggestions with regard to how to make your development environment safer.

Hope these steps work for you!

AbdulRahman Hariri : 21 Aug 2011 09:08 |  Tags: Ce Issues Lion Mac Osx Permissions Server Wordpress Zend |  Comments (0) |  Close comments |  Report a problem

Qualitative Research related blogs

Writing about web page http://merlien.org/news/qualblogs.html

A great list of qualitative research related blogs by Merlien institue. Can be found here.

Do you have any similar excellent resources? Share them please!

AbdulRahman Hariri : 27 Jan 2011 18:00 |  Tags: Blogs Qualitative Research |  Comments (3) |  Close comments |  Report a problem

Visual Understanding Envrionment

Writing about web page http://vue.tufts.edu/index.cfm

The Visual Understanding Environment (VUE) is an Open Source project based at Tufts University. The VUE project is focused on creating flexible tools for managing and integrating digital resources in support of teaching, learning and research. VUE provides a flexible visual environment for structuring, presenting, and sharing digital information.

Wow. A really amazing and interesting open source tool. You have to check it!

AbdulRahman Hariri : 20 Jan 2011 01:44 |  Tags: Mapping Mind Understanding Visual |  Comments (0) |  Close comments |  Report a problem

Mendeley

Writing about web page http://www.mendeley.com/

From Mendeley's website:

Mendeley is a free reference manager and academic social network that can help you organize your research, collaborate with others online, and discover the latest research.

• Automatically generate bibliographies
• Collaborate easily with other researchers online
• Easily import papers from other research software
• Find relevant papers based on what you're reading
• Access your papers from anywhere online
• Read papers on the go, with our new iPhone app
• View more features…

Mendeley is one of the new software/services that provides advanced references management features.

What I liked in Mendeley

What I really liked in Mendeley is that:

• It can sync your references between multiple PCs/Macs.
• Allows you to read, annotate & comment on PDFs from within the software itself.
• User interface is very nice!
• Can be set so that it starts watching your resources folders, adding every paper/document that is added to these folder to the library itself while tagging these auto added documents as 'To be reviewed' so that you can review and confirm that every bit of information is correct.

If you have been using Endnote (like me), you will be happy to know that you can export your Endnote library to Mendeley directly. Ofcourse, this doesn't mean that you can't use Endnote at all if you swich to Mendeley. You can work on Mendeley and if for any reason you wanted to insert bibliographies from Endnote or for any other reason, you can export your final library to Endnote and use it.

Research & Decide yourself!

Lastly, I just wanted to know that although I see Mendeley as a good choice for referencing management, etc.. However, I don't want to influence your decision in anyway!

You should spend sometime comparing/researching whatever software you are aware of, for example, for me, I ended up comparing Endnote, Zotero and Mendely. I quickly took Endnote out of the equation for a number of reasons such as its lack of easy sync features and inability to edit PDFs within the software. Lastly, I ended up choosing Mendeley over Zotero because:

• Zotero is a Firefox plugin. Therefore, it relies on another software which really adds another variable into the situation that could go wrong. For instance, what if there were some problems in Firefox? What if Zotero become unstable or incompatible for any reason with one of Firefox's future updates? Lastly, what if Zotero affects Forefox's performance?
  
• Mendeley's ability to edit PDFs within the same software is just great!
• The ability to watch folders within Mendeley is nice!

Therefore, it really depends on your work style and the set of features you might require which can be available in a certain software and not in the others.

Do you use any of these?

If you are using one of the mentioned software, I would really like to hear your experience. There might be features that I am not aware of in any of these mentioned software.

AbdulRahman Hariri : 12 Dec 2010 22:10 |  Tags: Bibliographies Endnote Management Mendeley References Zotero |  Comments (6) |  Close comments |  Report a problem

NVivo 9 Tutorials

One of my friends told me that his friend suggested that he uses NVivo for management of sources and qualitative data analysis. I have never heard of NVivo before so I wanted to give it a try. I downloaded the software and installed but still didn't really have the time to give it a try.

Furthermore, while searching for relevant reviews. I found that there is a good number of people who have suggested the use of NVivo in Academic Research and most certainly by PhD students.

I am really interested in finding what others who have used/are using NVivo think about it. I know that there is a need for some coding, but since I am going through the new journal papers I am downloading I will probably scan be able to code quickly.

One of the advantages of using NVivo is that it allows me to see all the sources related to one node (Theme or topic). Which really saved time especially if you are talking about having 100s of papers in your library. Being able to assign certain parts of papers to different nodes/topics is a really nice and very helpful feature!

I don't want to waste a lot of my time learning about NVivo 9 and testing it until I know for sure that it can help. Therefore, I haven't started using it.

I am actually hoping that some members of staff or some visitors would shed some light as to if NVivo 9 is indeed helpfull for me as a PhD student or not.

So, if you have any experience using NVivo 9 or any previous version, please let me know how it was. Did it help you get better results? Was it worth it?

Below are a number of videos that explain certain basic parts in NVivo 9, in case you wanted to learn more about it.

Introductin & Overview

Importing Sources to NVivo 9

Linking Cases to Attributes in NViv

Connecting Sources to Demographics in NVivo 9

AbdulRahman Hariri : 09 Dec 2010 00:09 |  Tags: Nvivo Qualitative Research |  Comments (0) |  Close comments |  Report a problem

Thumbnails in Wordpress 2.9+ and 3.0+

Now that Wordpress added a thumbnail feature (2.9+), we longer need to assign custom fields and give them values each time we write a blog post. Insted, while writing a blog post, there is a small panel or block to the side that allows us to choose a thumbnail for the post.

However, for people like me, who have been using custom fields to show pictures for sometime, there is a decision to be made. Should we stick to the custom fields and just continuou using them or should we start using the core thumbnails featre instead?

Well, you don't really have to the choose one of these two, you will keep using them both. How you ask? Well, simply, stop using custom fields for any new posts you write and use the thumbnail feature to assign thumbnails to blog posts. Then, edit your templates and add some simple conditions so that Wordpress checks whenever a blog post is viewed if it has a custom field thumbnail or a core wordpress 2.9+ thumbnail. By doing this, your old blog posts thumbnails will still show and your new thumbnails, the one you assign using the new feature will also show.

Honestly, I was very worried about having to choose one of these two, and since I am not a programmer/developer/coder, I was worried that I wouldn't be able to figure this out. However, with some thinking and imagination and with the help of a number of great Wordpress articles I was able to use my thumbnails in my Blog homepage. Not only that, but using some of the new features related to thumbnails, I was actually able to set specific sizes for the different pages in my blog. For example, on my homepage, all posts thumbnails are 100px x 75px. However, when a visitor clicks on a certain blog post to view it, he is shown the same picture but in a different size, say 200px x75px. This is really nice and it's really simple to achieve.

As I said, I am not a programmer and I was able to figure this out with the help of the following resources. There is no reason why you shouldn't be able to get similar results :). I would also like to thank each one of those blog authors:

• Bulletproof Post Thumbnails in WordPress 2.9
• WordPress 2.9 : Display post image with backward compatibility
• Using The New Post Thumbnail Feature In WordPress 2.9
• The Ultimative Guide For the_post_thumbnail In WordPress 2.9
• New in WordPress 2.9: Post Thumbnail Images
• Everything you need to know about WordPress 2.9′s post image feature

If anyone (not good with coding as I am) wants to look at the code I have used in my template pages to show the thumbnails, I would be happy to share.

If you want to check what I was talking about, you can visit my Arabic Research Blog. Don't ming the language, but make note of the thumbnails then follow some of them to the post view page to see if the thumbnail's dimension will change or not. Please note that because some of the thumbnails are actually cropped, they might not show in a bigger size if you follow them to the post.

AbdulRahman Hariri : 07 Dec 2010 01:59 |  Tags: Blog Custom Fields Images Post Thumbnails Thumbs Wordpress |  Comments (0) |  Close comments |  Report a problem

Get Your Research Library Organised with Zotero

Writing about web page http://www.zotero.org/

Zoter.org:

Zotero [zoh-TAIR-oh] is a free, easy-to-use tool to help you collect, organize, cite, and share your research sources. It lives right where you do your work—in the web browser itself.

Honestly, I find it one of the best tools available for researchers. really!

Zotero video:

Check Zotero's website for more information.

Zotero's features:

• Capture Research Data
• Archive the Web
• Store related PDFs, files, images, and links in your library
• Take Notes
• Drag and drop bibliographies anywhere: into an email, a blog post, or any word processor
• Plugins for Word and OpenOffice make it easy to drop in references on the fly
• Zotero comes preloaded with all major styles, and thousands of additional journal-specific styles are freely available
• Get the best of both worlds: Work locally with your research materials and automatically sync your data between multiple computers
• Even without Zotero, you can access your collection from any web browser. You can even view your collection on mobile devices like the iPhone.
• Share your research with the world and make your library and collections public
• Create group libraries to collaborate with other Zotero users
• And Many more...
  

So, What are you waiting for? Get Firefox if you don't have it and give Zotero a test drive :)!

AbdulRahman Hariri : 05 Dec 2010 06:07 |  Tags: Bibliographies Citation Management References Research Tools Zotero |  Comments (0) |  Close comments |  Report a problem