User:Jshorb

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Current version of the student website is available here: ChemPaths, with the Wiki for it kept here: ChemPaths. It is now hosted by the ChemEd server and should be accessible all the time. Please click on the 'discussion' tab above to write on the User_talk page to give feedback if you go to the site. My quick references are here: JShorb_Refs.

Update 21 May 2009

This week Tim began working with me and he has made excellent progress in 'atomizing' the textbook. The textbook has now been broken up on the other wiki: http://wiki.chemprime.chemeddl.org. The newest development is a rendition of the PTL! Glossary. It brings up definitions when you hover over defined terms. It works really well in different OSs and browsers.

The content model for Alfresco seems to be falling into place very well. I look forward to being able to swap over to that system as soon as the video and molecules databases are functional.

Update 13 May 2009

The majority of the last month was in preparing for evaluation, content models in Alfresco and mainly updating the wiki. The textbook pages have been moved from this wiki to the ChemPRIME wiki, which I administer. Things on that front are going smoothly and this summer we have some good students who will be working with us to fine-tune the interactivity of the Textbook.

Today was spent updating the website to be more Search Engine Friendly. A site-map generator was added to the Joomla! backend and it was submitted to Google. This is mostly useful because it was found that the Joomla! default search did not search wiki pages. Normally this wouldn't be too bad, but most of our content is wiki-held. The site now has a fully functional Google Custom Search mechanism. It works really well, but has some interesting difficulties.

Mostly, it follows all links. I have the website set up to keep the same title on a page while a student meanders. For instance, if you are looking at Group IIIA element properties and you click on the PTL link for Aluminum, the site only changes the center frame (not any of the navigation, nor the title). This means we now have a copy of the PTL! Al page with the title "Group IIIA Elements." It makes for many repetitive entries with different names. This has been circumvented by giving Google a Sitemap so that it registers those pages with higher priority.

Some to-do items for making the site more user-friendly: PTL! should have a drop-down menu which give all of the elements. This will make them easier to find. I will see if I can make it a pop-in Periodic Table, but that probably won't be doable. Also to-do is to make the Quick-Reference list (what would normally be in the appendix of a book, or quick-referenced tables. SI-Prefixes, Thermodynamic properties, glossary, etc. For some of these things, we'll likely work with some of the things Matt has worked on.

Update 08 Apr 2009

I have succeeded in writing a modification to the aWiki software that pulls a certain version of the wiki (as of a certain date) - rather than always pulling the most current version! It was quite the circular-hack-job, but it works smoothly, and It took minimal change to Hassan's original code (only the config.xml file was changed in order to add the "date" field).

This makes me very happy because it was the last thing needed to be done to the website in order to make it ready for instructor use. Now I simply have to figure out a good way to simplify the process - or to teach the process effectively.

This Thursday (Apr 09) is the wiki-extravaganza! A few colleagues of mine are going to help Jule and I to get the textbook completely broken up and into the ChemPRIME wiki.

Unfortunately, it seems that 'include_content_items' extension does not work well with my new modified aWiki extension. That is okay, though, because I'm not using that one much right now.

Update 06 Apr 2009

Things have been flying in the development world - just not in the development log upkeep world... sorry. ChemPaths is nearing developmental completion. I can currently do everything that I wanted to have done - but some aspects need streamlined so that others can do them with less knowledge of the infrastructure! Some tasks that are milestone achievements for ChemPaths:

  • The bottom navigation bar is a crowning achievement for ChemPaths. It is the basis of the Pathway Flow, keeping students on track. I must acknowledge help from the creator of Extended Menu extension, Daniel Ecer. He helped out in hacking his extension for Joomla! into the navigation bar.
  • Xavier has been extremely helpful in getting all of the applets embedded which allow for inclusion of molecule viewers and dot density viewers. They work really well (except a minor problem in Safari). I also have been working with him to get AO viewers for all the various elements of the PT (I ran calcs for elements 1-18).
  • The usage of aWiki extension to handle all of our bridging between MediaWiki and Joomla! has been completed! It works great and I was given permission from the creator, Hassan Amouhzi to create new models for the extension. I have created a model for both wiki.chemeddl.org and wiki.chemprime.chemeddl.org.
  • All articles (or aWiki content) is scanned for element names and linked to their respective PTL! wiki pages. It should become fairly simple to extend this same replacement technique to any part of our Glossary, if needed. I want to talk with the WHG people first, though. I think I can incorporate their work in a straightforward manner.
  • There are two 'related items' lists now on the right hand side for additional resouces "From your textbook" and "From Elsewhere". These are aWiki textbook pages and other various articles submitted to ChemPaths by instructors respectively. While clicking on these other links, students do not lose their place along the path, as the bottom navigation bar remains intact!
  • Upon Login, instructors get to see additional information, including an additional "Related Items" menu for other resources found within the entire NSDL. I deemed that list to be too long and verbose for student use.
  • External websites are incorporated by a modified wrapper (iframe). They work really smoothly! It allows for instructors to include extra text (just like the original ChemPaths so very long ago) and keeps the embedded tutorial/site cleanly free of menus, while leaving the bottom navigation bar.
  • Dioscouri Designs wrote a great user group tool which allows for control over which visitors get permissions to do various tasks around ChemPaths. This is the last portion of the website to be tweaked. It all works, but I want to make the instructor interface as simplified as possible.

Much of my time has been taken up by working on the ChemPRIME initiative found at http://wiki.chemprime.chemeddl.org. I have been basically building that site from the ground up (after Jon initially installed mediawiki). It has been fun to integrate all of the things I have learned in PHP by working with Joomla! extensions to writing my own extensions for MediaWiki. ChemPRIME is up and runnning smoothly, and is incorporated nicely into ChemPaths.

To-do (but maybe not directly by me):

  • Build submission protocols. How do we get people to submit their own movies/images/articles/molecular structures to our databases?
  • Refine the Menu-Builder tool (how instructors build pathways).
  • Work with Stephen Brandon, creator of MetaMod, to make our menu system as streamlined as possible. He has been greatly helpful thus far! I think we've nearly gotten that wrapped up.
  • Begin to build TONS of tutorials so that the site begins to reach critical mass of usable resources.

If you're interested in helping out in any of these tasks, please contact me!

Jshorb 14:21, 6 April 2009 (CDT)

Update 16 Feb 2009

There are tons of things to discuss, but for right now I wanted to just make a quick link to Development:ChemPaths To-Do List.

Update 26 Jan 2009

Today I spent some time recording 2 videos. One for students and one for instructors. Although the student one will likely have to get modified as features change, I wanted to make one as a 'selling point' for the ease of use of ChemPaths in studying (showing what Diigo does). The second one for instructors points out more of what ChemPaths offers and steers more directly toward integration with ChemPRIME.

Student Video demonstrating PTL! and Diigo: ScreenCast via Jing

Instructor Video about wiki pages, the textbook, and editing: ScreenCast via Jing

I will notify you that my skills at narrating are fairly poor, and at judging how to end before the 5 minute time-slot is up. But, as a proof of concept, I think it works well. If we see a need, we'll think about getting a different piece of software, but for now, Jing is really easy to use. I recommend it.

Please feel free to comment on my Talk page regarding what you see, or what things you expected to see. I also had my first run in with restarting the development server. As a note to myself: when restarting that computer I must shut down all instances of MySQL and restart the BitNami Stack using their controller script, using admin as the username (not root).

Update 23 Jan 2009

I have successfully moved portions of Chapter 1 of the online textbook over to the CoreChem namespace. I wrote a template which will go at the head of each page, and re-wrote the aWiki Joomla! plugin to block students from seeing the 'link-back' at the bottom of wiki-text-slurped pages. This allows for the student-interface to be all that much more clean. I have also re-wrote the 'Other ChemPaths Resources' side-panel to search for similar 'Exemplars' and for similar textbook pages. In this way, it's easier to delineate what sort of resource is available. I'm very pleased with the outcome, but for some terms there are just so many portions of the textbook that are relevant, we'll have to see if it needs to be truncated. You can see this at the development site, as I haven't made any of this live. I don't want to interrupt the Chem 311 course which is currently using the Wave Tutorial on the live site.

Soon I will be implementing the JUGA software on the development site, moving the rest of chapter 1 over to the CoreChem namespace and building some of those into the ChemPaths interface. I have been chatting with Chad a little about CPR, developing that for TA training and finally I have to get the evaluation criteria coming along.

Update 16 Jan 2009

The CoreChem namespace has been added to the wiki, and I have begun work on porting the content of the Chemistry book into finer grain at that location. I have also added a template file which will be ubiquitous to all pages. I have yet to begin to assign keywords or concepts, but the first few pages are fairly uncategorizable (for instance, CoreChem:What Chemists Do?) Over the weekend, Chem 311 stuff (CPR) will occupy most of my time, but I hope to begin categorization topics on Monday. I am enjoying the use of Joomla! tags thus far, and I like the ability to keep things editable while still hidden from student's view (the { reg } tags).

Also, I purchased a copy of JUGA (Joomla User Group Access) today, along with support. I believe that I will have everything I need to assign any tasks to any user I want shortly.

In other news, I heard back from Thomas Holme about the hierarchical concept map that the ACS exams institute has formulated over the past few years. I think we will be able to at least use some of that for metadata. I'll be getting a copy of it early next week. Plan on hearing about it at the next NSDL meeting!

Update 15 Jan 2009

ChemPaths has completed it's first update. I have successfully ported over a new snapshot from the development server to the live server. It was completed in about 5 minutes, so the process is quite streamlined.

Current discussion topics at the ChemEd DL General Meeting circled around where data should go. What content should be at the ChemEd Collaborative (here on the wiki)? Where should exemplars be built/stored? What sorts of things should be built in or stored on Alfresco? These are all great concerns. It requires a structured, planned response & community discussion. Thus, I have created ChemPaths:Introduction. I will hash out ideas there, and anyone is welcome to comment!

Update 08 Jan 2009

I have now successfully ported the ChemPaths site to the hosting server: chemed.chem.wisc.edu. Now development will continue on the development server, but there will be a stable snapshot in production at http://chemed.chem.wisc.edu/chempaths. The backup and porting process was surprisingly easy! I have also changed all the links within the ChemEd DL wiki. Let me know if you find a broken link.

Along the lines of the Wiki - I have spent a lot of time documenting how the ChemPaths site works. These How-To pages can be found at: ChemPaths:How-To. Feel free to have a look.

Also added to the wiki is a Tech Group meeting, included here for quick reference: Development:TechGroup:Meetings.

On the Alfresco front, I have added the integration between Joomla! and Alfresco so that users that are familiar with the Joomla! frontend can actually access all of the Alfresco database via the ChemPaths page. I'm working to get permissions worked out so that we know who did what and when. The next Joomla!/Alfresco will include a single-sign-on sort of protocol so that Joomla! can just use the usernames of Alfresco. We'll see how that works out.

Update 05 Jan 2009

A very small amount of hacking (but many hours of reading webpages and code!) has resulted in a fully functional Wiki to Joomla! interface! Now, editing and version tracking may be done by the controlled interface of the ChemEd DL wiki, while student interface can be done with the ChemPaths webpage. The 22 Dec update has a link to the sample page. It looks really excellent. I wish that the wiki pages didn't have to look so marked up, but they really do not get too convoluted, and at least the markup is readable. (words like tab and slide are most of the muck-up). This week will be a lot of page development.

As I begin to flesh out the examples within the wiki/ChemPaths content, I will begin to generate a manual of how this works. The first page of the manual is here: ChemPaths:How-To.

Update 22 Dec 2008

A lot of background work is being done moving pages within the registered area of the site. Some other things I wanted to do is to test out various wiki-to-Joomla! extensions. This will be done using the Joomla! Sample Page.

Update 12 Dec 2008

The Related XML Module was completely finished today. I even have it available as a Joomla! Extension (not on their website, but available in case anyone happens to be running Joomla! and wants it). It queries NSDL, caches the page's search on a daily basis, and then I have it set up to delete the cache each day using a cron function.

It works really well, so far. Now I have to look into modifying this so that it queries Alfresco, and possibly gets keywords from pages on the wiki. Now I feel good enough about how things are looking I'll start to build the content mostly.

Update 10 Dec 2008

Nuts and Bolts are almost completely under control for the new website! Yesterday the 'previous' and 'next' menu navigation code was completed (a modification of the Joomla! Extended Menu module). Today, a nearly completely redone version of the Joomla! Related Items menu was used to create a new NSDL search side-menu. This means that when an author writes a webpage and presses save, the text is scanned, keywords are assigned based on content, and then the NSDL query menu uses those keywords (trimmed and cleaned up) to get a list of resources from the NSDL search engine.

I did, however, discover a problem with the NSDL XML files, though. The schema is outdated and does not validate, and there is no mention of encoding. This results in my being unable to actually open the XML file from their site. Note: I can interpret their xml when downloaded to my computer, and I can access other site's xml files just fine. I think it's an encoding problem. I have sent a report to them and should hear back shortly (they're pretty quick). Once that is done - I want to extend the auto-generated keywords to generate keywords for the Wiki pages (so that NSDL resources are paired with textbook information) and then work on the CSS for the menu system I have done with the Prev/Next.

Update 08 Dec 2008

ChemPaths now has extended Jmol capabilities including dot density diagrams, 2D diagrams, and all of the Molecules 360 info. Things are finally seamless between multiple applets and it's looking great! I'm putting probably more effort than I should into finding a good navigational tool for going between pages. It's my last gritty detail to work out before ChemPaths is a production-level tool.

Although it's not 'production level' yet, I am of course working on producing my first full pathway: Atomic Structure. Building off of the Wave Tutorial developed for 109H f08, I'm trying to use the Jmol applets effectively. A few pages (outline form) have been built, and they will begin to be fleshed out. I unfortunately cannot determine how to best navigate between articles, which is very frustrating. It seems like it should be easy.

Update 26 Nov 2008

This is just a quick post to let everyone know that we are aware of cross-applet problems within the installed Jmols on ChemPaths. Please go ahead and check out the formatting and how it would work to insert various applets and leave comments as to what you would like. The problem of having buttons working for the wrong applet (or the mouse being frozen between multiple applets) is currently being fixed. I'll post when it's done.

Update 25 Nov 2008

Many, many bugs were fixed, the site now embeds really nice movies and even JMol from Xavier! It is really becoming very easy to build pages that look very, very complicated. Take a look at the site! (link in 19 Nov update)

Update 19 Nov 2008

Current development site is looking really excellent. All the bugs in navigation have been worked out, and the site hast tested positively on FireFox (Mac), Safari, IE7, IE6 (menu looks different, but works) and Mac IE5 (menu doesn't drop down, but it's at least usable). If anyone would like to check out the top navigation bar for me, that would be great. The link to the site is below.

On the other front, I have chatted with John about how to build the navigation set-up, after putting in a bunch of sample pages (such as the Wave Tutorial mentioned earlier). This should be showcased in John's talk on Friday, so that gives me a working deadline. This should be easily doable and I plan to have the first full tutorial up by today/tomorrow. For now, take a look at the Periodic Table Live! embedded page, as well as the Gen Chem Textbook page.

ChemPaths Development Site

Note: Began to develop a quick hack-job of a WHG using the WikiBot. This was not completed because it is not extremely necessary, but would just be a 'nice' thing to have. If anyone has a good handle on php, it would likely only take a few hours to finish. I just don't have the time to monkey with it (meaning learn the necessary functions and their syntax - it's just a bunch of search and replace php functions, but I don't know php variables well enough yet).

For Test Purposes: ![chemeddl: Temperature]. 

[chemeddl: Temperature]

Update 12 Nov 2008

The staging website is moving along really well. There was talk with John about making different pathways that run parallel, with different emphases, such as bio, materials, fundamentals, etc. and I believe I have found a way to make that possible. Overall, the site is looking good, and running much smoother than the old one.

I have implemented a Wiki Hyperglossary-like feature to the site. Any words placed in brackets when building sites is automatically linked to the ChemEd wiki and the associated pages. It looks to be very promising. I hope to have a sample page up by tomorrow's meeting. The only last thing to do is to figure out how to put the pages into the navigation scheme. Once I've done one, the rest should follow very quickly. At least the overhead is fairly minimal!

The Wave Tutorial should be up as soon as I can get it. Hopefully by tomorrow lunchtime.

Update 11 Nov 2008

Things have been in a consistent state of change. The development server is up and running. The installations to the server have been documented in hardcopy in the individual lab notebooks kept for each server (and Janice Hall's notes were condensed into the chemed.chem.wisc.edu log book/lab notebook). I have been rebuilding the website on the staging server, chemed2.chem.wisc.edu , using Joomla! open source website content management system. It has a few very useful features, such as seamless integration of wiki pages, within the website. This means that the course textbook pages that Jule has been updating can be seamlessly integrated, while still leaving the student immune to needing to navigate through the wiki.

I have now fixed all the website 'looks' and am figuring out the last bits of the awiki component that inserts wiki pages. Now I am beginning to look at the best way to navigate. Then it is a matter of re-inserting the pages I had already made into this content management system. This should be fairly straightforward.

Much of my time recently has gone into refining the use of Calibrated Peer Review (CPR) for the 109H class. It ended up being shot down by the student board, so the work will be used for next semester's course. But that took up a good chunk of effort. Things are finally back to the website at hand. A lot of the development work that went into the original ChemPaths website is paying off in a large way - making the website user-friendly has been much easier this time around (and I wouldn't say the last site was too user friendly at the end).

Update 15 Oct 2008

The next exam is coming up, a few students are beginning to use the course Diigo site, and I'm beginning to re-build the server. In order to make things as seamless as possible during the transition of the ChemEd DL to the Alfresco server, I am trying to get the ChemPaths database to run off of Alfresco. Instead of messing with the current server, which houses websites for other ChemEd Group people, we're going to begin the hosting on a development server. Then, once this gets stable, then the database will simply be shipped off to the JCE/ChemEd DL server to merge with the existing ChemEd DL, managing the external resources available there. This way, there will be no duplication. It's very exciting, and needs to get done fairly quickly! I have started server-logs (paper) to keep track of this transition stage.

The new server will house a copy of Alfresco, a copy of the WikiHyperGlossary, and ChemPaths. The transition should be fairly straightforward, but then these things always seem to appear that way. Jon has been very helpful in getting things up and running, so we'll see how the rest of the week pans out.

This weekend will be MACTLAC in Dubuque, IA, so I am prepping for that conference, where ChemPaths will make it's debut as the subject of a joint poster with Xavier.

Update 06 Oct 2008

Yes it really has been a month already. Things in the class are going very well, albeit fairly low-key for development. The students are using Diigo, but not actually for their own uses. It seems that they are more using it as a 'give me information' tool, as opposed to an interactive resource. Without the leeway to use points to encourage students in this course, things are not moving too quickly. I do have a few students who are going to use Diigo as part of their Honors Project, so that will be an exercise in generating some feedback.

I am working on a few different uses of online communities with faculty, students, courses, etc. to come up with ways of organizing and displaying these online resources. Mostly trying to delve into how to facilitate this interactive resource which ChemPaths will draw from. I am considering using Alfresco for my content management. I had a good discussion with Robert, and since my data is stored in XML format already, it shouldn't be a large switch. We'll see how efficiently things can be accomplished. It would be great if it was used as a repository for all the external sources, and then it can be more easily integrated into the ChemEdDL.

Coming up soon: MACTLAC conference in Dubuque, IA on the 17 October. See some of you there!

Update 03 Sept 2008

The rest of yesterday and today were very productive! I completed work on a few new pages, and looked over them with John. I got the CCA snapshots installed onto the server, created poster images for all the videos for CCA2 and CCA8, and redid all videos to have the snapshot picture and "Click to Play" text (Thanks to David and Jon!). I also finished up the Diigo enrollment pathway, and had a number of people test it out. In addition to that, I've created a Diigo group for the course and created the assignment which will return the first set of feedback. So far, things are looking good. Tomorrow is finalizing the order of the wave tutorial, and then sending out the e-mail to students.

Update 02 Sept 2008

Okay, the school year is underway. Although there has been work in making more ChemStones (webpages), I haven't posted too many updates. To be honest, I was hoping to have feedback from people about the pages as they were made and updated, but the energy that went into keeping this log, my "Updated Pages" pathway, and redoing the home-page became a waste as there hasn't been any posts or e-mails regarding changes from the at large community. I will therefore keep the Update Pages link without any modifications.

I have started discussions with a few people from BCCE and the start of the semester/ACS has slumped productivity. Instead of having my final path completed, I will have a few minor tutorials which will try out different features throughout the course. Waves and particles will be this Friday. More updates later.

Update 11 Aug 2008

edit* If anyone has discovered a good way to create nice web-ready graphs, let me know!

I created a number of new ChemStones today. According to my flow chart, I am approximately halfway through making all of the sites. I also had good discussions with both John (User:Jwmoore) and Xavier (User:xavier). Mostly John and I discussed additions to the site and a themed path that can vary, chosen by the individual. I am interested in trying to create a happy balance between size of the webpage and creating flow. The pages are ending up larger than we had originally considered.

Xavier and I discussed the Molecular Workbench and what options I have for using creations from there. Unfortunately, there seems to be no way to make a website that is interactive from that. They are against making MW into an applet because of the power of the Java Web Start for authoring - I may see if they would be willing to implement an applet exporter, though. We also discussed all the possibilities for the WikiHyperglossary and how that would be accomplished from our end. I hope that gets rolling soon.

I haven't created the new "Updated Path" (where all my creations are up for critique) yet. I want to get a few more up there before I create the path.

Update 08 Aug 2008

Today I revamped some data entry pages to use HTML entities so that things processed more reliably (and safer!). I also made a first attempt at putting cover images on the QuickTime videos. With David and Jon gone, though, small hiccups were made to be insurmountable. I moved on to making things a little more safe. A lot of correspondence needed to be caught up, so I opted to make sure that the web interface was safe and reliable - which it is now. I am currently working on a method for backing up the xml that is created by my interactive path-builder so that things don't get over-written as people use it simultaneously.

Note to self: xml_pp is a great tool for making xml files much easier to read.

Over the weekend I hope to have most of Chapter 5 cemented into place.

Update 07 Aug 2008

I have discovered a redundancy in the XML coming from NSDL search. I contacted a few people at Cornell to see what should be done with the problem. I also created a few more pages today which are available under the "Update Aug. 7" pathway from the homepage (link at top of this page). I also created the Pathway drop-down list as well as reworked the main pages so that they require a password in order to use certain pathways. This will be necessary as students begin using the website.

I did a lot of work into figuring out how to do a tracking button that would create a bookmark for students. Let me describe it: suppose a student follows an NSDL link and likes what they see. They then want to make that accessible later without having to remember which set of links they followed. A way of bookmarking this page for later studying would be ideal - but it is also forbidden for me to access external cite URLs (for good reason which I will not go into). Thus that idea is not going to work. For that, I may have students use Delicious, Diigo or something similar. I have contacted Delicious for any suggestions/ideas. As we are always stating: try not to reinvent the wheel. I have found some good references that talk about integrating del.icio.us (to use the more formal name) into Moodle - although further search makes Diigo look a little more conducive to classroom dynamics. If this is fairly simple then it will add an entirely new dimension to the use of the online course. There is also a social bookmarking module which can be incorporated into Moodle Moodle Social Network Bookmark Activity . If anyone has heard of anything, let me know!

I am considering moving the ChemPaths 109H pathway into the 109H Moodle course. Other than just creating a link to my site, I'm not sure what the difference would be unless it would be easier to link to other Moodle activities (thinking about the bookmarking tool).

I have yet to have any comments on the Recent Changes page. Please feel free to edit the comments!

Oh, and my site started to have robots crawl through it, and they will frequently look for a favicon.ico file and a robots.txt file. So I made those. I have a JCE icon file now (as well as my own ChemPaths- CP icon). If you want to have the JCE one, let me know. It is not that great (not as nice as the pink erlenmeyer currently on JChemEd - but I couldn't figure out how to steal that one).

Update 04 Aug 2008

My time at the BCCE was extremely helpful. In addition to attending many seminars, meeting with other people within the Chemical Education circle was invaluable. I had a chance to explain my project repeatedly to different audiences. By hearing other options which are similar to my project, it helped to cement the unique goals of my own online resource. There are a number of people who are very interested in the expandable way ChemPaths operates.

Unfortunately, I did injure my leg immediately before leaving for the beautiful walking campus of IU-Bloomington. After re-pulling the same tendon (or muscle) in my calf, I will be going to the clinic this afternoon. I only inform this update log as it means that all updates to the website will be occurring remotely (on my laptop) for the next few days as there is no internet access where I am staying.

The current goal is to get the rest of the pages for my module up, and to get the WHG running. Once these two things are accomplished, that will be a good level of polish to test this fall.

Update 27 Jul 2008

Currently attending BCCE at Indiana University at Bloomington. If you are there and have been following along the growth of ChemPaths, then send me a message and we can meet up!

Update 24 Jul 2008

I have been successfully adding content to the website. I met with David Pieper, who was helpful in getting videos into my content pages. They don't have the nice preview photo, yet. I'm hoping to chat with Jon about that this afternoon. I also added a 'recent changes' link on the home page, so that new pages can be reviewed. I would love it if people would leave comments on the pages of any typos, content mistakes, or simply re-wordings. Or new content page suggestions. They're being added all the time. So far, so good, though. I feel the time crunch and things have been moving fairly quickly.

I have been in contact with Bob Belford, who has been very helpful. Even if I don't get it implemented before the test phase, I think that the Wiki Hyperglossary holds a lot of promise for the future of the project.

I've also been looking into CPR (Calibrated Peer Review). It is an online peer review website that uses wiki-like technology. for subject matter like the structure of the atom, it may be a nice addition to homework from the Moodle course (which John Moore recently set up).

This coming week is the BCCE in Bloomington, IN. I'll be attending a few seminars, and it sounds like I'll get to meet a lot of people. If anyone outside of Journal House or ICE reads this: look for me at their booths. If I'm not there, they'll probably know where to find me next.

Update 17 Jul 2008

All the bugs have been worked out of my static site generators (both for the SamplePath and the ChemStones pathways). I have uploaded them to the ChemEd server as well. The password required portion of the website does not seem to work with the way Apache is set up on that server. I will have to look at that once Janice's course has completed.

I have also signed up for Google Analytics which monitors usage of the webpages. I want to have it monitor the site for awhile to see what sorts of information is available. It may be useful in statistics later, or maybe not. Either way, it is extremely easy to include and we'll see how it looks.

Update 16 Jul 2008

I changed the WebText pages to being mostly static. Well, they have static content instead of using xml for the content. I still have them generating their side-bar navigation on the fly.

I was going to avoid creating the "Create a Pathway" part of the website, but it was best to do it now. In order to show ChemPaths to people, it needs to have a Path through all of the webpages. Now, it is easy to create a new path through all the various sites, along with teacher notes. It works really well. I really like how the teacher sees the exact same layout as the students, but with entry fields instead of text. I'll have to have people try to build a pathway as soon as I have a few more pages up.

On the content side of things, I fleshed out my flow of pages in the past few days, and started building some sites. I also found Chemistry Heritage Foundation website and added a number of their bibliographies to my database. All of my "Off-Pathway" sites will be external for now. So far, so good.

Late night edit: The site is now static with a script which can auto-update all the WebText files! I just need to cross-reference the ChemStones and Path XML files to be sure the numbers are in sync after all the modifications recently.

Update 13 Jul 2008

It is done! I now have a fully working page generation and linking website. This includes dynamically created text websites as well as off-site ones. This section (as it heavily modifies the site files) is also password protected. I will be hosting it on the ChemEd server as soon as I implement Perl on that server. I am finally officially to the point of simply using what I have to create webpages.

From the back-end, there are a few other items which are not of immediate concern but are on my wish-list:

I want to turn the site from being all dynamically generated to being static pages which are re-generated once per day or so.
I want to expand my xml management portion of my website to generate a pathway (but since we only have one right now, it is not necessary to figure that out now).
I want to make my thumbnail images link to larger versions of the same photo. They currently all resize to the same small size so that the webpages load faster. This may be bad later when people will have graphics that are too large. This can be handled on a per-image basis for now.
Create dropdown list of sites for navigation bar.
Limit the number of 'nearstone' sites that are shown in the side-bar.
Develop a "Like This" button for the navigation bar.
Continue talking with Bob about Wiki Hyperglossary (it is sounding very promising).
Incorporate an "ALT" into the image uploader.

Update 09/10 Jul 2008

I chugged through a long night and managed to get a CGI webform working which will generate entries into the database for ChemStones. This should be fairly simple to modify and get it working for all 3 databases (ChemStones.xml, PathX.xml, and WebText.xml). From there, I won't have to worry about linking webpages and can simply build them and have them auto-linked together.

I am also now in contact with Bob Belford at UA-Little Rock regarding Chemistry Hyperglossary usage on the ChemPaths site. Unfortunately it's built in MySQL and PHP... but I'll bet I can learn a few new data processing languages! Why not?

Update 09 Jul 2008

Apparently there are a few issues with Perl/XCode for my laptop. These are being ironed out so that I can get CPAN to work correctly for updating my Perl code. This is going on in the background while I read about the history of the atom. In addition to the paper copy of my references, I decided to list those on the website JShorb_Refs. It is useful because it actually auto-generates a link if you include the ISBN!

Update 08 Jul 2008

It is completed! The basic layout of the navigation and frames for the website was completed this morning. I have an archived copy of this located at ChemPaths-Jul 8th. Now the last part of tweaking is to make the page content. It is currently hard-coded (hence the backup) and now I'll be playing around to make it dynamic. The question now is whether to write a webpage that uploads them, or just type them by hand. There are plenty of ready-to-use modules out there to make the webpage easy to develop.

Oh - and I got rid of using the dtd files mentioned earlier. They are still fairly valid, but with all the namespaces I was using, I didn't want to try to keep updating the dtd to make it validate. Perhaps at the very end this will be worthwhile, but my xml files are fluctuating too rapidly.

Update 07 Jul 2008

After a week's worth of vacation, I am back. I have drastically changed mindsets on the use of JavaScript to do much of my website. Over the last week, I have now decided to utilize my many years of Perl usage and access my XML files in that way. This has proven to be a quick switch-over from my previous website, and things are going quite well so far. I am having trouble using Perl to access the NSDL.org website's xml page, though. For some reason the site returns extraneous information as a header and footer that do not need to be there, and are making it hard to parse. I have a work-around in place, but it is not very pretty (and may not be the best solution in the end). I will simply remove everything up until the beginning of the official xml, and after it. It will likely slow things down. Contacting NSDL may be helpful, but not as the only question I have. Perhaps I'll include it in a later e-mail.

ChemEd Server update: stereochem now has admin access so that Erik Dunning can have admin resources on MySQL there.

Update 26 Jun 2008

Today at the NSDL meeting, I will be bringing along the JCE DigiDemos ToC. I wanted to have this link available here, as well as my own text version of the DigiDemos Keywords here.

In adding the content pages, I am currently working on developing Physical Properties of Matter: Electromagnetism and immediately followed by the Coulomb's Law page. In order to do this, and have an easily added on webpage, I want to use a CSS (done! heavily modified from a free one at freeCSS.com) and then use a MySQL database to manage the content. This way each page can be generated with updates. I will likely use Perl as I have a lot of experience with that language.

Also, if anyone has any good ideas on possibly using an XML for the Paths, but using SAX for the ChemStones database, that would be good. For now, javascript/XML works fine, but if this gets quite large, then I may want to change it down the road.

Thanks!

Update 25 Jun 2008

The top bar is called the “Navigation Bar” and will be used to progress along the path. At this point, the code for using that is fairly solidified. It updates the bottom frame while still allowing off-site navigation (useful for linking to NSDL or ChemEdDL).

Data is stored in two XML sheets: ChemStones.xml and Path1.xml. Their corresponding layout is below:

paths.dtd 

 <!DOCTYPE ChemSteps [
       <!ELEMENT ChemSteps     (steps)>
       <!ELEMENT stone         (id,summary,admon)>
       <!ELEMENT id            ($PCDATA)>
       <!ELEMENT summary       ($PCDATA)>
       <!ELEMENT admon         ($PCDATA)>
 ]>

ChemStones.dtd 

 <!DOCTYPE ChemStones [
       <!ELEMENT ChemStones    (stones)>
       <!ELEMENT stone         (id,title,abstract,url)>
       <!ELEMENT id            ($PCDATA)>
       <!ELEMENT title         ($PCDATA)>
       <!ELEMENT abstract      ($PCDATA)>
       <!ELEMENT url           ($PCDATA)>
 ]>

The path is denoted by an ordered xml sheet, such as Path1.xml and refers to objects in ChemStones.xml. Thus, a given ChemPath can be in a different order, and also skip or include any number of ChemStones along the way. To keep updating simple, The ChemPath controls what the students see for their individual viewing screen along the Naviation bar, without changing any information about the actual content page. In the example above, the Title is taken from ChemStones -> title, the information for the student (“The starting page below...”) is taken from Path1 -> summary and the admonition (“Good Luck!”) is taken from Path1 -> admon. The content frame (Google) is taken from ChemStones -> url. The buttons in the navigation bar take students along the path to the left and right. Link title

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