ChemToolBox and ChemPup ToDo's

-add new screenshots and update ChemPup features list
-upload ChemPup-1.0.1
-remaster ChemPup-0.2.6 and re-upload (note diffs)
-generate MD5 checksums for ISOs
-trim the fat on ChemPup-1.0.1
-start a proper changelog
-test shopping-cart
-build axs ChemPup kits
-produce multisession DVD
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ChemPup-0.2.6 Released at ChemToolBox.com

So I have a functioning web site (www.chemtoolbox.com) with a download manager called remository that is pretty easy to use and tracks download totals. To date, ChemPup-0.2.6 has been downloaded 8 times since its release on 10.7.09 (2 days). I posted a forum thread at the official puppy linux forum (http://www.murga-linux.com/puppy/) and have 85 views in just 2 days. I am hoping for feedback and may ask for some when my downloads total reaches ~20.

ChemPup-0.3.0 is bothersome. I am very excited that I got Avogadro to work!!! However, at a bit of a cost. First the success story. I downloaded a copy of Barry K's UPup which includes the ubuntu-debian repositories in his powerful new package manager. This was accomplished through project "Woof" which is essentially a project aimed at making puppy buildable/extendable with any existing linux repo. Very cool! I used UPup to download Avogadro, analyze it's dependencies and add them as obtainable and install everything automatically. I had to deal with one "lib" problem (I wish I had documented it earlier) and then had Avogadro running in UPup in about an hour. Then I had an idea....prompted from some research at the forums. I saved my UPup session and then renamed the .2fs save-file to the standard pup_save* format so ChemPup (based on Puppy 4.2.1) would read it. I then booted ChemPup-0.2.5 (the devx version) and loaded the new save-file and voila! I had a new version of ChemPup with Avogadro working.

However, after testing several other programs, I found everything worked except one: BKChem. Grrrr. This is not an acceptable trade-off in my view as BKChem is by far the best 2D structure editor I have found for linux. I believe the problem lies in the python libs added with Avogadro, since BKChem runs with python. I spent a couple hours trouble-shooting this but since I am not a trained CS-guy (i.e. self-taught) I have yet to correct the problem. In the mean time I am thinking of offering both versions and explain the deficiencies in each. Essentially, the addition of Avogadro is very beneficial for people that want to do computational chemistry and JChemPaint is still available as a 2D structure editor. However, for those who want to produce higher quality 2D structures for use in documents or publication, the BKChem version is better.

TO DO:

1. Fix the BKChem/Avogadro incompatibility issue
2. Find a silk-screen CD package
3. Find/Buy 3D glasses
4. Work on a multi-session DVD
5. Assemble packages and make sell-able on chemtoolbox.com
6. Make donations page on chemtoolbox.com (remember to show $flow)

ChemPup USB boot

Ideally ChemPup would be delivered on a 2GB USB flash drive that had a small (128MB) windows readable (VFat or NTFS) partition that has the ChemPup user guide, quick-start guide, tech support info etc. Then upon reboot, the flash drive will already be inserted and the bootable ext2 partition with ChemPup will boot up and they will know exactly what to do for the initial boot. Well it seems that this is very possible, but not necessarily fail-safe and instead depends on the hardware configuration. I am unsure if it is important which partition be "first" on the drive, but on initial test it seems that windows is only happy reading the first partition. Likewise I had trouble on at least one older computer to boot ChemPup from the second partition, but when first in line it was okay....meanwhile, at school I have found ChemPup on partition 2 boots without any trouble. So I am encouraged, but again, I will need to have "back-up" plans that can be rapidly deployed if a user has trouble with older hardware.

ChemPup-0.1.5 ready for beta testing

I now have a ChemPup "full" version that I am happy enough to beta test. The .iso is 454MB which is kind of in the middle for a puplet based on my survey of the official puplet page, though most attempt to be smaller than 100MB. However, I decided to leave devx.sfs which adds some extra but will facilitate growth for now, and of course as mentioned previously the "full" version comes default with openoffice3.0.

Notes on making the puplet:

I had difficulty figuring out how to retain most of the aesthetic settings like desktop wallpaper and icons, and additions made to the menu. I sort of cheated and simply renamed the puppy-fun module to "Chemistry" in /etc/xdg/_root_.jwmrc and /etc/xdg/menus/jwm.menu but I left the rest of the settings pointed to puppy-fun.menu. Then I simply edited puppy-fun.menu to read name "Chemistry" I removed all categories listed and replaced with "Chemistry." Afterwards I needed only generate appropriate .desktop files for each new program added (just like with ubuntu/debian) and I was in business with all my chemistry programs added to the main menu.

During the "puppy remaster" process I then had to make sure to copy /etc/xdg over to the /tmp/etc/ folder at the appropriate time. Likewise, in order to preserve the rest of the desktop configurations, I copied any files I thought would be "config-like" from /root to /tmp/root at the appropriate time. By this procedure, I save all desktop configurations but do not jeopardize any Xorg, keyboard, video, mouse settings for the next user who will likely have a different hardware configuration.

I played around with burning a multi-session DVD or CD and although initially successful, it seems that I only can change the settings once and save to the disk which then closes the session. So now I believe I will offer ChemPup on a CD or a 2GB ext2 flashdrive and encourage CD users to save the personal file and ChemPup.sfs to a flashdrive as well. As such, I took my own 2GB flash drive, dual-partitioned into a 1GB vfat32 and 1GB ext2 to which I installed ChemPup-0.1.5. I selected mbr.bin for the master boot record step since I had done a complete reformat.

I am now working to set up www.chemtoolbox.com to be a mostly functional site that will at least a) not look hideous and b) host the ChemPup-0.1.5 .iso file as well as a few other support documents.

ChemPup-0.1.3

I have temporarily abandoned implementation of Avogadro in my ChemPup project. I was wasting too much time for a "proof-of-concept" product. Now I am thinking of dividing the project into a ChemPup "full" and ChemPup "lite" set. The difference will be that ChemPup "lite " will be released as a downloadable puplet (hopefully under 400MB) that I will host on a basic descriptive website. ChemPup "full" will be at least 700MB (I think) and will be burned "open-session" to a DVD (I hope). The full version will come with extra documentation, and OpenOffice3 will be bundled in along with several other features (see below). I also am hopeful to put together a useful spreadsheet template that will have relevant (solvable) chemical equations with descriptions. I also hope to write a simple program to calculate molecular weights since I haven't found a quick-and-easy one yet. So here is the list of features for each:

ChemPup-0.1.3 "lite"

Office Productivity: (Default Puppy Linux)
Abiword - word processor
Gnumeric - spreadsheet
mtPaint - image editing
SeaMonkey - web browser

Chemistry Programs:
Periodic Table Wallpaper
Nomen - generates 2D structures from chemical names
WebMolCalc - web utility to calculate formula weight, combustion analysis, and isotopic distribution
BKChem - 2D structure editor
JMol - 3D molecular viewer
ChemPupDoc - documentation on using above programs.

ChemPup-0.1.3 "full"

Office Productivity:
OpenOffice.org-3.0 - full office productivity suite compatible with MS Office
JabRef - reference manager that syncs with OOO3
SeaMonkey - web browser

Chemistry Programs:
ChemPup-lite programs +
GElemental - periodic table packed with information on each element
Avogadro (if I can get it working some day)
OpenBabel - chemical file-type converter
SciFinder Scholar (maybe) - must have site.prf file added from school administrator
ChemTool - spreadsheet template with useful chemical equations
MassCalc (need to write) - molecular mass calculator

ChemPup-0.1.2

I recently had the idea to assemble a Puppy Linux "Puplet" that would be configured with software useful for an undergraduate chemistry student. Considering I know nothing about programming and I am still very new to Linux, this is proving to be a challenge...but I have had success so far.

ChemPup-0.1.2 has been developed from Puppy Linux 4.21 running with 512 MB ram in a VBox machine on Ubuntu-9.04 and so far includes most of the packages I have envisioned in this first generation build. The following is the list of added packages:

Office Productivity Suite:
OpenOffice.org-3.0

General Chemistry:
GElemental - a gtk+ periodic table of the elements with loads of information on each element
MoleCalc - a molecular weight calculator (runs in WINE)

Organic Chemistry:
BKChem - a 2D structure editor with .mol and .odt (openoffice) export capabilities
OpenBabel - a command line molecular file-type converter that handles over a dozen formats
WinDNMR - a dynamic NMR simulator (runs in WINE)

Need:
A suitable 3D molecular viewer (I want Avogadro which includes a force-field minimizer)

Plan to Make:
A slick spreadsheet template (OOCalc) that has useful conversions (mole to gram etc) and equations
Detailed documentation to maximize usage of the system (since most US Students don't know Linux)

Additionally I need to figure out what programs I should cut out to save space, if any, considering OOO is adding most of the extra weight. I will probably remove devx.sfs.

Building in the existing packages (listed above) was fairly straightforward....I needed to install Python, WINE (which I found as a .pet on the Puppy Forum) and a few other package dependencies that I cannot recall.

Update: In order to run BKChem it needs python 2.3 or later and after checking with > python --version <> ./configure; make; make install. Unfortunately these programs must be installed before python so I had to reconfigure python and went ahead and downloaded the upgraded 2.6. Python is a bit large so I removed the old version...2.6 also took several minutues (10 ish) to compile and install. Afterwards bkchem.py runs from command line with > python bkchem.py < in the working directory. I then easily created a bash script to start the program, made it executable with chmod 777 and added it to the desktop with a logo icon to make a simple point and click execution.

The real trouble has been with Avogadro. This is a nice, intuitive 3D molecular viewer and force-field minimizer program that I test-ran on Ubuntu and was quite happy with, however, unlike with Ubuntu, I do not have a prepackaged .deb (.pet) for Puppy and will have to build it from source. Avogadro has several package dependencies, some of which I am having trouble with building as well: Qt4, Eigen2, CMake, and OpenBabel are all required before you can compile and install Avogadro. I installed OpenBabel and CMake okay (I think), and Eigen2 supposedly only need to be unzipped and it is ready to go (although they don't say to which directory it belongs so I stuck it in /usr/local/bin). Qt4 on the other hand has proven very difficult and I also found that I had the wrong version of CMake!! These programs (OpenBabel, Qt4, and even CMake) took a long 20-30 minutes of compiling time each. So long as I can get a user-friendly 3D molecular viewer I will be satisfied with this first release.