Temporary fix for publications list on abandoned public site

[dentarthur]

Re my Q5 and Q6 and answer to them here:

FLAMEGPU/FLAMEGPU2#354 (comment)

Q5 publications list here includes some missing from public site:
https://flamegpu.github.io/publications/

Could this be updated to include last few years and made easily accessible? (Does not include some very useful papers from 2017-18 and hopefully others even later).

Some links from main publicly available list are broken and should be fixed:
http://www.flamegpu.com/publications

Q6. If I am pointed to a markdown version of publications list to update I could add a few items I have come across though I imagine it would be better to generate direct from a bib file that somebody should have.

@mondus said:

Q5: The website is out of date. We have a prototype new site which we will deploy with the first release of FLAME GPU 2. New papers will be published on the architecture when we are ready.

Q6: Our new site will be github driven so you will be able to issue a pull request to add publications. For now you could add an issue to https://github.com/FLAMEGPU/flamegpu.github.io/issues which is an old port of our current site which will be used as a starting point for the new one.

1. I understand from answer to Q5 and others that focus is on getting an initial release of FGPU2 leaves little time and requires avoiding distractions.

2. Meanwhile I suggest at least adding a link from outdated list to:

https://flamegpu.github.io/publications/

Here is a sample broken link.

This works from unpublished new site:

http://www.paulrichmond.shef.ac.uk/cv/publications/pedestrians.pdf

But this does not work from published old site:

http://www.paulrichmond.staff.shef.ac.uk/publications/pedestrians.pdf

Both are for:

Richmond Paul, Romano Daniela(2008), A High Performance Framework For Agent Based Pedestrian Dynamics On GPU Hardware, Proceedings of EUROSIS ESM 2008 (European Simulation and Modelling), October 27-29, 2008, Universite du Havre, Le Havre, France

Several others similar. I assume wholesale link rot when folder moved from /cv/ to /publications/.

At present the old site conveys the impression of a project abandoned around 2012.

3. Plus an "edit on Github" link to markdown for that page.

4. However that page appears to be written in html with broken rendering on Github:

https://github.com/FLAMEGPU/flamegpu.github.io/blob/master/_pages/publications.md

See section for:

"Publications Using FLAME GPU

2014+"

After 3rd reference (Konan S), there are 9 list items (starting with de Paiva Oliveira and ending with Hermellin, E.) broken on github but readable at:

https://flamegpu.github.io/publications/

5. Not feasible to submit edits to html pages on Github in view of above. Needs to be markdown version that jekyll then generates html from. That can presumably be generated directly from a bib file used to maintain list.

6. BTW direct link to publications works but it is inaccessible via the "About" drop down menu (on my browser). That doesn't matter as long as there is a PROMINENT direct link from public site to a reasonably current list of publications (with a "back soon notice from the phoenix ;-)

7. I also suggest adding item numbers (within section labels). If there is a markdown version with a sample item number I can add pull requests for numbering the rest, also for adding doi and perhaps some missing items as I catch up with the literature.

8. PS Do you consider BioDynaMo as another potential general purpose ABM for GPUs platform?

"BioDynaMo: an agent-based simulation platform for scalable
computational biology research"

bioRxiv preprint June 8, 2020. https://doi.org/10.1101/2020.06.08.139949

It dismisses FGPU along with others:

"SBML integration.Existing agent-based simulators [5,10–20] do not integrate with
the well-established SBML standard. Therefore, users of these simulators do not benefit
from the large collection of available chemical reaction networks described in SBML
format. In contrast, BioDynaMo allows users to simulate SBML models in each agent."

FGPU is included as item 20 in the "10-20"!

If BioDynaMo or any others are comparable for general purpose ABMs it could also be a good idea to add a section for listing them as earlier FGPU papers mention FGPU as the only such framework available for GPUs.

Anyway, SBML could be added to the future input output list for FGPU along with hdf5.

Recent papers about ABM frameworks sometimes display incomprehension about FGPU, eg:

Koschienko MASS CUDA s2.3 p142
Y. Demazeau et al. (Eds.): PAAMS 2019, LNAI 11523, pp. 139–152, 2019.
https://doi.org/10.1007/978-3-030-24209-1_12

A Survey on Agent-based Simulation using
Hardware Accelerators Jiajian Xiao et al
arxive [cs.MA] 1807.01014

Incomprehension is encouraged by lack of access to a current publications list.

9. Richmond Paul, Coakley Simon, Romano Daniela(2009), A High Performance Agent Based Modelling Framework on Graphics Card Hardware with CUDA, Proc. of 8th Int. Conf. on Autonomous Agents and Multiagent Systems (AAMAS 2009 link), May, 10-15, 2009, Budapest, Hungary

Correct title is:

A High Performance Agent Based Modelling Framework
on Graphics Card Hardware with CUDA
(Extended Abstract)

I tracked this down despite broken link and different page numbering from the published proceedings:

http://www.paulrichmond.staff.shef.ac.uk/publications/aamas09.pdf

But was unable to find a full version. If there is one, please provide a link. Otherwise I suggest to save others the time of looking for it by adding a note:

(The 2 page Extended Abstract is the only version available).