Friday, July 16, 2010

PDF World

Well, as I delve deeper into my early research career, I have noticed my fondness of using open source software more frequently. I have already posted about Ubuntu and Wubi and about the frustrations of using Word with EndNote or Mathtype. Mendeley Desktop seems to be the best citation/source organization software which you can upgrade for more space and shared collections starting at $4.99 a month. I plan to explore Latex here in the next few weeks and want/plan on using it for my PhD thesis. Latex seems to be the best documentation software for large documents with lots of equations/graphics/etc. Also, you have the freedom to pretty much do whatever you want, especially with the layout. You are not restricted to certain rules that Word employs.

So this post is about the familiar and useful document form called PDF. When I hear PDF I automatically think Adobe Acrobat. Adobe is probably the leader in PDF software, but they do not own the PDF name. There are plenty of free readers out there including Adobe's Reader and the one I am currently using Foxit. Both of these software allow you to do basic stuff such as opening a PDF file and some editing. I know Foxit will allow highlighting, comments, notes, arrows, etc. with their free version. Of course when you use these features Foxit places a watermark on the page which is no big deal for me since I am using these features for personal research purposes obly. I don't need to print them out, and the watermark does not affect any major function. This is great news for those of us who only need PDF software for simple things as these.

If you need more features I would consider buying the software which there are plenty of choices and the price isn't too bad (from around $20 to $100 or more). I would also look into your school to see if they have licensed versions and/or discounts for students and faculty. There are usually student versions available at a large discount which contain most needed features too.

Anyways, we sometimes need a few more features such as deleting pages, rotating certain pages, combined PDFs into one document, rearranging pages, splitting a PDF into several separate PDFs, creating PDFs, etc. I have googled and searched thinking to myself that surely there is some free software that someone has kindly taken their time to develop that would do these things. (Down with tha man!!) Because unfortunately Foxit only rotates every page in the document, and you cannot save it at its rotated position. I am not sure about Adobe Reader or any other free reader.

Upon browsing the www, I did stumble across a somewhatofa PDF edior. (Here is one of the forum discussions where I found some ideas

(oh, and sont click on the docq link, it seemed kinda fishy)

This software is called PDFTK Builder, and it is absolutely free. Another bonus is that this software has a GUI for us programming challeged people because there is the orginal PDF toolkit builder that is programming based)!!

This PDF toolkit is great. It allows you to combine PDFs, rotate pages, and much more. I will update as I figure out more. I just combined two PDFs with ease!

So my point here is not to convert everyone to open source software but to be open minded and available to many platforms. It is great to know the most common software such as Adobe, Microsoft Office, Windows, etc, but it would be well worth investing time into to some other versions such as Mac OS, Linux, Latex, etc. Imagine a future employer or collaborator asking if you know how to use such and such software in an interview or meeting and/or being able to put a multitude of knowing various software. This, IMO, is a great self promoting/marketing tool. Also, it would be nice if a collaborator began a research project in a certain program suite which you could pick up easily or would already be somewhat familiar or even an expert in so as to avoid much repetition or frustration. However, all of this is not necessary just a suggestion and my experience because one could quite possibly run into a pitfall of trying to learn too much and spreading oneself too thin. Just take your time and experiment with all sorts of programs.

As for future post, I plan to cover some more in Mendeley now that I have been using it for a few weeks. I also plan to cover LinkedIn, a professional "facebook" type networking tool. A few other things that I would like to cover are my experience with Latex and an Ubuntu update. as well as OpenOffice, Google Documents, and drawing programs such as Google SketchUp.

Tuesday, July 13, 2010


Ok, finally I got close to what I wanted to accomplish with posting the old posts. I have changed my mind and decided not to post about my research on this blog. I will, however, create another blog for that purpose. The blog will focus mainly on tips for problems that I have run across in research, dealing mostly with computer technology.

One update for the Word problems. I think I am going to attempt to write the PhD thesis in Latex because my thesis plans to be quite large and I don't want to deal with Word crashing like it likes to so with large documents.

Also, I kept having issues with Word and MathType. Word kept crashing unless MathType was disabled. I finally figured out a solution through my colleague Michel Akiki. Word or Microsoft has the option to install a repair kit. So that is what I did, and well, it actually found the problem and fixed it. It actually worked!! Just another idea if you run into problems like I have had and the registry or template fix doesn't help.

Oh, I have also read that Word can get funky when it is opened and the computer shuts down to restart in order to complete the automatic updates. This has happened to me so I disabled the automatic download, installation, and restart.

Old Posts

My friend and colleague, Dr. Tony Saad, shared with me a new, well new to me, software that organizes your sources. It combines Zoterowith EndNote! However, I am still learning it and working with it, and it seems that it may have issues with Microsoft Word. The software is called Mendeley Desktop, and it's absolutely free! It seems to be pretty powerful as you can drag and drop PDFs into your library and Mendeley will automatically pick up the information. You can also import your Zotero library and have the software "watch" folders and your Zotero library for automatic updates when you add sources to these locations. I haven't fully explored its power yet, but it seems to be a permanent solution to both EndNote and Zotero. We'll see as I don't have much time to mess with this new software. Another cool thing is that Mendeley will rename your PDFs anyway you specify which is a huge time saver. You can also link and enter information easier than Zotero, and you don't have to worry about if the download citation thingy works or not. Needs more investigation!!

PS I just found out how to edit posts, duh!


I have always been interested in OS for computers. I can remember the early days (for me) when DOS was the essential way to use a computer. Then came along the early versions of Windows (I think 3.0 or so was the earliest I can remember). I remember still having to use DOS though for certain games or programs, so Windows was not nearly as dominate as it is now. There were also some Macs around which had similar windows OS's. Anyways, about a year or two ago I found out about Linux and its many versions or flavors. I tried it out in our lab, but ended up being frustrated because I felt it was so hard to install a simple Adobe Flash Player for Firefox. However, I really felt like I could get use to it, and I really enjoyed this new OS because of its freedom and it reminded me of the good ol' days. The versions I was exposed to were Fedora, Redhat (the pay for version, Enterprise I think?), Ubuntu, and Kubuntu.

Anyways, I have always planned to install some Linux version on my home computers so that I could mess around with it (I also even would like a Mac OS too!). The other day, my good friend and colleague, Tony Saad, told me about Wubi. Wubi is an installer for Windows that automatically installs Ubuntu on your computer with dual boot and separate partition. If you don't like it, you can unistall with no traces or problems. So I have tried it out, and it turns out I am writing this blog post from Ubuntu!! I think this is wonderful, and should spread this use of Linux to others such as myself.

Here is the link:

FRIDAY, MAY 7, 2010

Ok so the problem with Word was bigger than I thought, but fairly easy to fix. Every time I tried to save, close, or edit the document (change add-ins, since Endnote was not appearing) Word froze and was not responding. I thought, great, going to spend all day trying to figure this out, and I do not want to have to reinstall everything.

However, with some googling, I found that this is somewhat of a common problem, especially after updates. It seems that either the Normal.doc template is corrupt or the Windows Word Data registry becomes corrupt. Here is a link that easily solved the problem for me (registry edit fix it for me).

Word Registry Edit

Update- 6-14-10

I'm glad I posted this because it has happened again! This time on my desktop. The problem now seems to be with Mathtype and/or OriginPro8. Here are some additional links to the same post earlier.

Normal.doc Template Reset

Registry Backup

PS My laptop is running Windows 7 (updated from Vista), and my desktop still has Vista at the moment.


First off, I finally have submitted into writing a blog.

Update: 5-5-2010

Anyways, after a few years of negelct, :), I think I now want a site where I can publish my research work and ideas since I am getting older and more experienced in the field. I also would like to post scientific information or hints/tips which is inspired by my good friend and colleague Tony Saad and his blog Please Make a Note.

Moved Blog

Alright, so I have switched my blog over to my new, more professional gmail account. My old account is still active, I just won't update it.

I will repost my old posts so that nothing is lost. The purpose of this blog is still to share research information such as my research progress and tips and tricks I come along during my research path.