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Introduction

Example of Hexokinase

This graphics engine is built with the help of SDL2, Bullet physics, OpenGL and some more stuff.		File:Opengl Tiny.jpeg File:SDL logo20 sm.png

Projects

Glycolysis

This is intended to be a labtool helping educating university students in metabolism. It is an interactive learning tool for teaching methabolism.

• Platform: PC, linux Ubuntu
• Architecture: 64 bit linux running on a 64 bit hardware.
• Graphics: Gallium 0.4 on AMD PITCAIRN (DRM 2.43.0, LLVM 3.8.0
• OS: Linux Ubuntu 14.xxx
• Software used
  • OpenGL (Open Graphics Library) API for rendering 3D vector graphics.
  • SDL 2.0
  • Bullet physics (bullet-2.82-r2704)
  • Glew
  • OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics software based on the OpenGL Shading Language (GLSL) specification and released under the MIT license.
  • Lua (lua-5.1)
  • Freetype (freetype-2.4.12)
  • Assimp (assimp-3.3.1)
  • IMGUI (imgui, v1.51 WIP)
  • pthread (POSIX thread solution/libwinpthread (port to windows)

• Planning to use
  • RDKit

Molecules

• GLucose (α-D-glucopyranose)
  • Glucose on Wiki
  • on ChemSpider
• fructose-6-phosphate
• fructose1_6_bisphosphate link : ChemSpider
• Phosphoenolpyruvate (2-(Phosphonatooxy)acrylate)
  • Phosphoenolpyruvate on Wiki
  • on ChemSpider
• Pyruvate
  • on Wiki
  • on ChemSpider

BioMolCraft (Date:19/11-18)

Preparing updates for coming use in a lab (Dec 4 -18).

DoD - list of tasks to fulfill before the event:

• Reset/Restart
  • clean load ?
  • [Done] only restart test
• [Done] Randomize positions
• [Done] Cleanup menus
  • [Done] Remove/disable all menu selections that is not in real use of the actual test
• [Partly] Cleanup bugs
  • make sure no bugs are left, this can only be done with thorough testing
  • some kind of memory leak when restarting several times.
  • [Partly] the exit dialog needs to be removed and replaced by ImGui, since it is a long delay on current solution
  • [Done] make sure only molecules are moveable objects
• better mouse ptr precision (low prio on this task)
• [Done] Windows 10 (a must if the lab no longer have linux)
• [Done] Splash screen when starting up the program, either use Plane, or ImGui (low prio)

BioMolCraft 2.0 (Date:2/7-19)

• big molecules big footprint in memory, how to handle this?
• raytracing, can it be used in animating the process?

DoD- list of tasks to fulfill before october

• make GameLogic2 work again,

- part of this is to have testing framework up and running for stage class

BioMolCraft 2.1 (Date:24/11 -21)

Issues

• links to external molecule page doesn't work anymore. The link has changed.
• drag and drop of molecule names works poorly

Any time to fix these problems?

Other

Ideas

sequence Diagram of LP

An error occured in the PlantUML extension.
command 'java -jar plantuml.jar -charset UTF-8 -o "/home/u230599544/domains/vhundsport.se/public_html/LPWiki/images" "/home/u230599544/domains/vhundsport.se/public_html/LPWiki/images/uml-9565814d5d564fa898dd6111b94fae0b-46ff9813722c7e820cb6fd7656ee65c5.uml"' returned status code=127

Building for Windows 10

• Add freetype

 freetype download

• build result in linux:

./objs/libfreetype.la
./objs/.libs/libfreetype.lai
./objs/.libs/libfreetype.so
./objs/.libs/libfreetype.la
./objs/.libs/libfreetype.so.6.10.1
./objs/.libs/libfreetype.a
./objs/.libs/libfreetype.so.6
peter@ironman:~/projects/LP/freetype-2.4.12$

• Build from powershell works
• Text works, menus works, Gtest?

• building lua

should be built from powershell, needs to be manually built for each source code file, see script I made included in the src folder. then link it all by running >make mingw (from powershell)

• mingw libs needed to be included in Debug folder when running the program:
  • libwinpthread-1.dll => /c/MinGW/mingw64/bin/libwinpthread-1.dll (0x64940000)
  • libgcc_s_seh-1.dll => /c/MinGW/mingw64/bin/libgcc_s_seh-1.dll (0x61440000)
  • libstdc++-6.dll => /c/MinGW/mingw64/bin/libstdc++-6.dll (0x6fc40000)

Binaries for Windows 10

• Resources.zip
• LP.zip
• Debug.zip
• Lib.zip and contains:
  • biomolcraft.bat,
  • config_lp.lua,
  • Glycolysis.exe,
  • Glycolysis_config.lua,
  • libgcc_s_seh-1.dll,
  • libstdc++-6.dll,
  • libwinpthread-1.dll
• Lab-2018.zip

Building for Linux OpenSuse 13.2

• Distribution: openSUSE 13.2 (Harlequin) (x86_64) 64-bit
• Building details openSUSE13.2

Download Glycolysis binaries for openSuse 13.2

• Glycolysis.tar.gz
• BEvent.tar.gz
• lib.tar.gz

Building for Linux CentOS Release 6.7

• Distribution:
• Kernel: Kernel Linux 2.6.32-573.26.1.el6.x86_64
• Gnome 2.28.2
• Building details CentOS Release 6.7
• Run Glycolysis

Binaries for CentOS Release 6.7

• BEvent_centOS_6.7.tar.gz
• Glycolysis_centOS_6.7.tar.gz
• Glycolysis_centOS_6.7_ver2.tar.gz (version 2)
• Glycolysis_centOS_6.7 (version 3)
• Glycolysis_centOS_6.7 (version 10)
• Lib_centOS_6.7.tar.gz

• Glycolysis_GL31_DEPTH24.tar.gz
• Glycolysis_GL31_DEPTH32.tar.gz
• Glycolysis_GL42_DEPTH24.tar.gz
• Glycolysis_42_DEPTH32.tar.gz
• Glycolysis_GL42_DEPTH24_NOMULTISAMPLE.tar.gz
• Glycolysis_ver11_GL42_updated.tar.gz
• Glycolysis_ver11_GL42_mito.tar.gz

Building for Linux CentOS Release 7.0

• glxinfo
• glxgear

• LD_LIBRARY_PATH = /home/peter/projects/tmp/lib:/home/peter/projects/tmp/libOS

>export LD_LIBRARY_PATH=/home/peter/projects/tmp/lib:/home/peter/projects/tmp/libOS

Download binaries for CenOS 7.0

• Glycolysis_stripped4.tar.gz
• libOS.tar.gz
• LibOrig.tar.gz
• Glib.tar.gz

Other

OLD Getting started