File:Screenshot from 2022-03-29 08-22-52.png

2023-01-14T16:57:16Z

Peter:

Main Page

2023-01-14T16:39:06Z

Peter:

== Introduction ==

[http://brorssonsite.com/LearningPlatform/hexokinase.html Example of Hexokinase]

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This graphics engine is built with the help of [http://wiki.libsdl.org/FrontPage SDL2], [http://bulletphysics.org/wordpress/ Bullet physics], [http://opengl.org OpenGL] and some more stuff.

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[[File:Opengl_Tiny.jpeg]]
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[[File:SDL_logo20_sm.png]]
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== Projects ==

=== LearningPlatform ===

=== 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)
** [https://en.wikipedia.org/wiki/Glucose Glucose on Wiki]
** [http://www.chemspider.com/Chemical-Structure.71358.html?rid=7d472045-8ad6-4b5d-80e2-6d001db73481&page_num=0 on ChemSpider]
* fructose-6-phosphate
* fructose1_6_bisphosphate link : [http://http://www.chemspider.com ChemSpider]
* Phosphoenolpyruvate (2-(Phosphonatooxy)acrylate)
** [https://en.wikipedia.org/wiki/Phosphoenolpyruvic_acid Phosphoenolpyruvate on Wiki]
** [http://www.chemspider.com/Chemical-Structure.2907208.html?rid=f320ad46-2953-407f-8fae-5059c6a90bbf&page_num=0 on ChemSpider]
* Pyruvate
** [https://en.wikipedia.org/wiki/Pyruvic_acid on Wiki]
** [http://www.chemspider.com/Chemical-Structure.96901.html?rid=7cddb65a-6e75-42f9-999c-b7dbbcb0306c 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]]

<uml>
title Sequence of LP
participant LP
participant View
participant Stage

LP -> View : TestSignal
LP <-[#blue]- View : TestSignalCfm

</uml>

== Building for Windows 7 ==

== Building for Windows 10 ==

* Add freetype
[https://www.freetype.org/download.html 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 ===

* [http://brorssonsite.com/LPWiki/images/6/67/Resources.zip Resources.zip]
* [http://brorssonsite.com/LPWiki/images/1/1a/LP.zip LP.zip]
* [http://brorssonsite.com/LPWiki/images/0/09/Debug.zip Debug.zip]
* [http://brorssonsite.com/LPWiki/images/c/c8/Lib.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
* [http://brorssonsite.com/LPWiki/images/2/24/Lab-2018.zip Lab-2018.zip]

== Building for Linux Ubuntu 14.xx ==

== Building for Linux Ubuntu 16.04 ==

== 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 ===

* [[Media:Glycolysis_smaller.tar.gz|Glycolysis.tar.gz]]
* [[Media:BEvent.tar.gz|BEvent.tar.gz]]
* [[Media:Lib.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 ===

* [[Media:BEvent_centOS_6.7.tar.gz |BEvent_centOS_6.7.tar.gz]]
* [[Media:Glycolysis_centOS_6.7.tar.gz |Glycolysis_centOS_6.7.tar.gz]]
* [[Media:Glycolysis_centOS_6.7_ver2.tar.gz |Glycolysis_centOS_6.7_ver2.tar.gz (version 2)]]
* [[Media:Glycolysis_centOS_6.7_ver3.tar.gz |Glycolysis_centOS_6.7 (version 3) ]]
* [[Media:Glycolysis_ver10.tar.gz |Glycolysis_centOS_6.7 (version 10) ]]
* [[Media:Lib_centOS_6.7.tar.gz |Lib_centOS_6.7.tar.gz]]

* [[Media:Glycolysis_GL31_DEPTH24.tar.gz |Glycolysis_GL31_DEPTH24.tar.gz ]]
* [[Media:Glycolysis_GL31_DEPTH32.tar.gz |Glycolysis_GL31_DEPTH32.tar.gz ]]
* [[Media:Glycolysis_GL42_DEPTH24.tar.gz |Glycolysis_GL42_DEPTH24.tar.gz ]]
* [[Media:Glycolysis_42_DEPTH32.tar.gz |Glycolysis_42_DEPTH32.tar.gz ]]
* [[Media:Glycolysis_GL42_DEPTH24_NOMULTISAMPLE.tar.gz |Glycolysis_GL42_DEPTH24_NOMULTISAMPLE.tar.gz ]]
* [[Media:Glycolysis_ver11_GL42_updated.tar.gz |Glycolysis_ver11_GL42_updated.tar.gz ]]
* [[Media:Glycolysis_ver11_GL42_mito.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 ===

* [[Media:Glycolysis_stripped4.tar.gz | Glycolysis_stripped4.tar.gz]]
* [[Media:libOS.tar.gz |libOS.tar.gz ]]
* [[Media:LibOrig.tar.gz |LibOrig.tar.gz]]
* [[Media:Glib.tar.gz |Glib.tar.gz]]

== Other ==
[[OLD Getting started]]

=== transfer files on internal network ===

[[Media:Client-server.tar.gz]]

=== Resources ===

[[Media:GLycolysis-process.png]]

LP

2023-01-14T16:36:57Z

Peter: just testing out

I am starting to add text here

LearningPlatform - User contributions [en]

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