Status Report on the Development of the Rogue Science Website

July 2, 2008

It is hard to believe this is the 11th anniversary of my website. What began in June as a desire to efficientize the code by removing redundant nested tables from my templates has evolved into an entire recoding of all my page templates from scratch! I was finding it very difficult to figure out what part of the page I was editing with tables within tables within tables… I redid the site using style sheets with a much cleaner and efficient code.

Of course I couldn’t leave it at just that. The perfectionist in me reared its ugly head and I redid many of the graphics as well. At first I just wanted to strip out the evil JavaScript that I use for the rollover effect in the header graphics. I figured out how to do it better with style sheets, but that required editing the buttons. Since I had Photoshop open already, one thing led to another, and before you know it I completely redesigned the header, added a better font to my bar graphics, optimized my file sizes, and renamed the slices.

My psd files were starting to become a jumbled mess of disorganized graphics with weird names that was taking longer and longer to load. I started to organize the layers and rename the slices, which is what led to me redoing many of the site graphics. The more I learn about Photoshop, the more I can do to my graphics. The filenames of the graphics now make more sense, at least to me, and by using multiple psd files to hold my graphics my computer is no longer threatening to choke and die when I edit something.

When I originally recreated my site templates in 2007, it was with the intention of having standard elements for the header, side navigation column, and content area to enable me to make edits sitewide. However, each of the four major sections of Rogue Science had its own flavor of template, and as I edited those I made alterations to the basic structure of the template. As a result I ended up with numerous revisions scattered about the pages that all should have been part of the template. This left me with some pages better optimized than others, and I could no longer run a single search query to replace elements in batch.

When I started digging in the code, all those nested tables kept getting in the way. While the site does use a little CSS to control things, I mostly relied on inline declarations. This does not make for very efficient code, so I started to move things to my external style sheet. Once I started to edit the style sheet, I found the code was jumbled there too. Back to school I went to teach myself more effective CSS design, and before I knew it the entire site was redesigned with div blocks rather than tables.

The site is much easier for me to update now, and I think it looks better than ever. I am by no means a designer, and I lament the time spent on frivolous features such as presentation when I could be researching more chemistry and actually adding content to the site. Even so, presentation is nearly as important as content because if users can’t find anything on your site they won’t use it, and if it looks terrible they will assume the content is too.

In the second major revision to my site around 2001 I added a search form element to the navigation column. In this time I don’t think the search script has actually ever worked. I more or less used the element as a placeholder and never actually installed a working search script. I may have had a working search script briefly, as I recall, but I hate relying on some buggy freeware cgi or php code that would take me a month to configure and learn.

This time around, because I was redoing the navigation template, I actually set up a working search feature, thanks to Google and their wonderful webmaster tools. The Google Custom Search feature only requires me to drop in the form code, while Google does all the work. I still have to configure some features, and I don’t much like the ad branding, but the end result is a largely labor free search engine that works. Google ads are infinitely better than the offensive and intrusive ads on every other website. I strongly dislike all advertisements, but for some reason Google have never bothered me. I think this is part of the success of Google, the ads are not flashy and “in your face” so to speak. I use the Firefox plugin CustomizeGoogle, which removes all Google ads among other things, so I never see them anymore. I highly recommend CustomizeGoogle by the way.

Of course, all of these changes, the style sheets, the graphics, etc., are to the template I build the site around. This means no one actually gets to see any of my changes. Before I update the site I need to add the existing pages content to the template. Now begins the manual process of pasting the content into each and every page on the site.

Jun 3, 2008

The last few months have seen many changes to the site, predominately to The Forum. The Forum has undergone a massive overhaul involving a complete wipe of the old database and the more than 4 years of code detritus. The new board has some interesting advanced features for social networking including user determined social groups, customizable profile pages with image gallery feature, tag cloud searching, and taggable threads.

I started collecting donations for the site at the end of May. The last few months have seen the site shut down several times due to excess resource use, and my host told me I will need to upgrade to a dedicated server. Those are quite expensive, and they involve more work on my end, but the alternative is no more Rogue Science. What to do? Hopefully I can collect enough in donations to cover most of the costs of running the site.

I went ahead and licensed the entire Rogue Science website under a Creative Commons license in May. I cannot in good conscience rail against the corrupt media and publishing industry destroying the copy rights of the people through twisted copyright laws if I use the same loathsome copyrights on the site. Copyrights are supposed to protect the people, not greedy corporations, a fact the government seems to have forgotten. Now Rogue Science uses an attribute-noncommercial-share alike license for all works on the site.

Feb 22, 2008

Most of my time in the last four months has been spent administrating The Forum, so little progress has been made on the Rogue Science website other than numerous minor corrections and edits. This has indeed taken far longer than I ever anticipated! There is so much to be done that I get swamped trying to figure out where to start, and as soon as I stop working on the site for even a few days I completely forget where I left off.

The 2D graphics have been completed for all explosive labs, and almost all of the 3D graphics are done as well. I uploaded all of the labs, 2D graphics, finished filling in the physical properties, and completed the master index of all explosive compounds. I have not yet uploaded the 3D graphics, even though I have been sitting on them for months now. Something bugs me about them, they are just not good enough for my standards.

I am still dismayed that the 3D graphics are too small to see, the file sizes are huge, loading all these files will eat up tremendous amounts of bandwidth, and all for what is basically eye candy. The real kicker is after all the hours of work I spent creating the animated 3D molecules I realized I should have made them an extra 100 pixels larger (300x300 instead of 200x200).

I think I will stick to a simple 3D static gif that is linked to an animated flash video of the rotating molecule, or to a JMOL page. This way I will not punish those unlucky souls still on dialup by loading a 300K graphic on every page. The site is already brushing up against bandwith limits as it is.

Speaking of bandwidth, the Rogue Science domain was briefly suspended due to excessive resource usage, largely due to The Forum. I have been asked to upgrade to a dedicated server, but at a significant price increase. The upgraded package is more than I can afford right now, so I will soon begin accepting donations to keep the site running.

Nov 4, 2007

After taking a little time off to enjoy the wonderful summer weather I am back on track to completing the website conversion. Over the last few months I have finished rewriting all of the introductions, completed all of the html files for energetic materials, created a new alphabetized index incorporating all of the synonyms for every energetic compound, and managed to find CAS numbers for almost every explosive.

Having every compound labeled by CAS numbers has already led me to identify 2 duplicate explosives listed under different names. The CAS numbers have opened a whole new world of reference information including many physical properties, molecular structures, and numerous additional synonyms.

Now the bad news. Even though I have all of the html files “done” I am still not going to upload them until I get the graphics finished. The entire site looks broken and foolish in my opinion with nothing but the same placeholder graphic repeated on every page. Better to hold everything until I make progress on the graphics.

Another problem that has taken me a considerable amount of time to figure out is compiling all the chemical synonyms in an alphabetized list. I have so many explosives that keeping track of all the names without missing anything is time consuming. I ended up placing everything in excel, but how chemical names are alphabetized is different from how excel or word alphabetizes things. I eventually figured a way to alphabetize all the chemical names as a batch that spits out url link code without me having to do much work. My discovery of a large number of new synonyms (after I finished creating my new index page) means I have to recreate the index from scratch.

I decided to withhold publishing my labs for the most popular explosives, TNT, RDX, acetone peroxide, etc., because I want to completely rewrite them, and add considerably more information about their usage and synthesis. With over 150 different energetic materials on my website, and likely hundreds more coming in the near future, and all the other content, I can’t exactly remain up to date on developments for compounds I have already published. However, a key few compounds are worthy of expanding. RDX for example has thousands of publications about it, and probably a dozen different methods of synthesis, but I barely scratched the surface when I wrote about it years ago. Acetone peroxide has received a surge of attention due to its media coverage, and I want to include every relevant publication that covers this explosive. I will only devote this effort to a small handful of explosives because every hour I spend on something I already have is an hour that could be used researching a completely new explosive.

Speaking of wasted hours, my quest to find a satisfactory molecular modeling solution has been tedious and time consuming. It seems I misplaced all of the original files created in my molecular modeling app. I still have all of the gifs, so I can easily recreate them, and I never did finish about half of the models, so there is much work yet to get those done. It is the 3D part that is causing trouble. I originally wanted to display all 3D structures as a short avi clip, but I really don’t like embedding movie files into a webpage because browsers never seem to support them right. I would love to display everything with Jmol, but embedding java in a webpage is even worse than embedding a video. I hate java scripts, and I always surf the net with java completely disabled because I don’t trust what the freaks and perverts will do to my computer with it running. I know my own website will not have anything evil in it, but I assume everyone has the good sense to do without java, so I don’t want to make it an important part of my site.

My best bet is to make animated gifs. Sounds easy, it’s not. For all of the sophisticated molecular modeling packages in the world, they sure fall flat when it comes to exporting different file types for displaying on the web. What’s the big crisis? I want my own custom background behind the molecule. No modeling package has an option for a transparent background, so I have to use pro grade video editing software to digitally remove the background. This is what they call chroma keying in the editing biz, or what you may be more familiar with as either “green screen” or “blue screen.” Because for some ungodly reason my 3D models use lighting and shading effects when exported as an avi file, the solid color background I want to remove via chroma keying is altered. Chroma keying software is notoriously intolerant of color variations, so I have to convert each video frame to a gif and remove the extraneous color pixels in Photoshop before reassembling an animated gif in ImageReady. Naturally I do all of these things in batch mode using macros as much as possible, but somebody has to figure out how to set up the batch steps beforehand. It would be a waste of my time to manually edit some 16,000 frames.

I may yet include a separate 3D section to display the molecules in Jmol, and include the original xyz/mol/pdb files for people to play with on their own molecular modeling app.

July 28, 2007

This week I am creating the new html files for all of the explosives labs and copying over the content from the old style. It took me a few days to set up a system of doing this, but now it is progressing quite smoothly. I still have about two thirds of the pages to create yet. I am still not publishing anything because the pages still need much more work to make them acceptable to my standards.

I need to redo all of the 2D molecular graphics in photoshop to make them adhere to my standard. Since wikithieves (morons who steal my content as their own without linking back to me) have been stealing my graphics, as well as my content, and passing it off as their own, I added a roguesci.org background watermark thing to each of the images. Damn wikithieves! It seems all of my newest additions never even had a graphic created to begin with, so it is off to the uni library sometime this summer.

Speaking of the library I need to acquire CAS numbers for all of the compounds on my site. The addition of CAS numbers is more to help me not duplicate my own efforts by researching a compound I already have information for. It has already happened at least once that I know of. There are so many synonyms of chemicals these days, and I have so many different labs on my website, that it may not be immediately obvious if I already have the compound in question. I always search my site before adding something new, but this is not foolproof. Hopefully listing everything by CAS number will eliminate any duplicate effort.

For some ungodly reason I cannot find the original references for all of the new explosives I added last year. The molecular structures and CAS numbers should be in those files, but they are long gone. I think all of the information may have been on my laptop that went screwy this spring. It was old, and free, but nonetheless valuable to me. To bad I am currently “between jobs” because I can’t afford a new one right now. I would quite thoroughly enjoy working outdoors on my laptop instead of being chained to my desktop in my stuffy office.

I should also mention I still have to do all of the 3D molecular graphics too. I originally shelved doing 3D graphics several years ago because of the large file sizes and high bandwidth consumed by the files. Now the file sizes, and their resulting bandwidth consumption, are not pressing issues. Still, that means I have to make over 150 animated 3D molecular graphics for the explosives alone. I still have not decided if I want to use an animated gif format, flash, or a more chemistry appropriate Chime or Jmol format.

July 15, 2007

Conversion is underway in earnest.  I am rewriting all of the introductions for my explosives labs.  Quite frankly my writing ability has improved significantly since much of the content was originally written.  The old introductions included more errors than I thought, and they tended to be a bit less formal than I would prefer.  I was hoping to finish rewriting all of the introductions last week, but it is summer time, and it is quite nice outside.  While I have finished all of the introductions, I have not actually added the content to the website.

July 4, 2007

The day is finally here, the official tenth anniversary of the day I first released my website on the world! I had hoped to complete the rollout of the new format of Rogue Science by today, but I scheduled a summer class I erroneously thought started after July 4, but which actually started at the beginning of summer semester. The class only ended last week, so very little is finished. I have eight more weeks until fall semester begins...

The templates for the pages have been done for several weeks now, I have most of my graphics in place, and the section introductions have been written for almost all sections. Now to port the content from the old site to the new site.