95 replies to this topic

[Mind]

Just another example of how this type of project is being duplicated elsewhere. This idea has been floating around for decades yet no one has "broke through" to capture a larger audience, to make the science of aging more understandable, accessible, and intuitive (you can find a whole lot of complicated schematics though). The is why we HAVE to succeed in jump starting it here!

[smilence]

thank you for share. I'll read it carefully

[Andey]

Andey, can you find out what software was used to create this file from Dr. M?

Hi )

Sorry, I didnt saw you message because it didnt contain quoting of mine.

I dont know exactly but this is an open PDF file. As far as I understand using Adobe Illustrator and Adobe Acrobat is way to go.
I have them on my PC, and I could easily change text on schema, move lines in AI etc. As far as you dont want to save result in pdf file then Adobe Illustrator is the main software you need (Adobe Acrobat can change text but not lines and boxes). Only problem that I see is that some original fonts are missing(at least on my PC with W8) so you partly loose text formating.

I have tryed to open content in AI and export it to Adobe Flash, attached AI and Flash projects + compiled swf.
If you dont have this apps I can export document to other AI supported types.
Adobe Flash also have AIR project option to work with that gives opportunity to create cross platform applications for iOS, Android, Blackberry etc

Main concern for me at this stage is that I dont understand what we want to achive at the end. If we want to change document a little, add Longecity credentials and export it to Flash document etc - this is not a big project and could be done in few afterwork hours.
If we want this than we need to contact Alexey and ask permission for that. I give his contact info to Mind, because Mind have credentials to speak for our community.

P.S. And...this is not a project really - I think we need to put more to this - may be check all links and add interactive descriptions to the documents etc. May be not on first approuch but at least we need do plan such thing in future.

Added: I cannot attach files directly, because site engine didnt allow such file types
Here is gdisk links
https://docs.google....1l2WWxXYzA/edit
https://docs.google....DlxdzQtWDQ/edit
https://docs.google....jFtVm9qYkE/edit

Please download it, and I will delete it from web access

Edited by Andey, 20 January 2013 - 10:57 AM.

[rikelme]

Hi All,

Tha Adobe flash is certainly in a decline and being replaced with HTML5, for several reasons. Even the Adobe has realized that and it already offers tools which instead of flash create HTML5 based applications (animations, games, etc). One of them is completely free, Adobe Edge Animate:
http://html.adobe.com/edge/

The interface of the Edge Animate is very similar to the one flash developers have been using when developing flash applications. So, who knows how to use Adobe Flash, he/she will know how to use Adobe Edge Animate.

Personally I am more a programmer than designer, but I might be able to find someone who can help. For this particular task, or call it a project, it might be a good idea to use a Trello (www.trello.com), which I find extraordinary and completely free project tracking tool (I'm not affiliated with it in any way). Using Trello, the project leader (manager) can easily create a list of tasks and assign them to a project team members. The progress of each task can easily be tracked, and everything (tasks, progress, assignments...) is at a glance, instead of posting here on forums.

I hope this helps a bit.

Cheers !

[Andey]

Hi All,

Tha Adobe flash is certainly in a decline and being replaced with HTML5, for several reasons. Even the Adobe has realized that and it already offers tools which instead of flash create HTML5 based applications (animations, games, etc). One of them is completely free, Adobe Edge Animate:
http://html.adobe.com/edge/

The interface of the Edge Animate is very similar to the one flash developers have been using when developing flash applications. So, who knows how to use Adobe Flash, he/she will know how to use Adobe Edge Animate.

Personally I am more a programmer than designer, but I might be able to find someone who can help. For this particular task, or call it a project, it might be a good idea to use a Trello (www.trello.com), which I find extraordinary and completely free project tracking tool (I'm not affiliated with it in any way). Using Trello, the project leader (manager) can easily create a list of tasks and assign them to a project team members. The progress of each task can easily be tracked, and everything (tasks, progress, assignments...) is at a glance, instead of posting here on forums.

I hope this helps a bit.

Cheers !

Thanks for heads up )
I am also sw developer (not web one) and we use JIRA+Agile for Project and bug tracking purposes, but completely free engine is a plus )
HTML5 will be also a plus. As I see this tast require only basic functionaly so I think it will not too hard to implement it with new software.

But again - I didint sure what we are going to do with this project, and we need Alexey Moskalev and may be previous designer permissions to alter their schema.

Edited by Andey, 21 January 2013 - 09:12 AM.

[YOLF]

Hi All,

Tha Adobe flash is certainly in a decline and being replaced with HTML5, for several reasons. Even the Adobe has realized that and it already offers tools which instead of flash create HTML5 based applications (animations, games, etc). One of them is completely free, Adobe Edge Animate:
http://html.adobe.com/edge/

The interface of the Edge Animate is very similar to the one flash developers have been using when developing flash applications. So, who knows how to use Adobe Flash, he/she will know how to use Adobe Edge Animate.

Personally I am more a programmer than designer, but I might be able to find someone who can help. For this particular task, or call it a project, it might be a good idea to use a Trello (www.trello.com), which I find extraordinary and completely free project tracking tool (I'm not affiliated with it in any way). Using Trello, the project leader (manager) can easily create a list of tasks and assign them to a project team members. The progress of each task can easily be tracked, and everything (tasks, progress, assignments...) is at a glance, instead of posting here on forums.

I hope this helps a bit.

Cheers !

Hmm... I will definitely check this out. I was thinking about doing it in 3D as a game environment, but if this is something I can learn easily. It looks like it may be the way to go.

[rikelme]

And regarding the PNG layers... yes, it can be done that way, but I think that vector graphics should be first pick here. PNGs and other raster graphics are not scalable (zoomable) as vector graphics is. Here we have only rectangles, lines, arrows and text - no fancy images, logos, etc that would require raster graphics. Vector graphic can be zoomed in / out without limits and it would be still in crystal clear quality.

Just my 2 cents

[rikelme]

So, can someone sum up the action plan? Who is doing what at the moment? Do we even have the clear goals?

[YOLF]

I'm offering to try to learn Edge. I was working on it as a graphic designer, but I was finding it difficult to fit all the info into a digestible form. So I was going to do it in 3D and try to figure out how to convert it to a game environment that could be ported to web. AFAIK, it was just me doing what I could with PSCS2, AEP7, and a handful of 3D apps. What can you do? I don't know AI, flash or much to do with web design beyond simple html and maybe a little java script for specific tasks. So if you can do anything like that, I think we can get something done. Mind is the Defacto project manager.

[rikelme]

I'm offering to try to learn Edge. I was working on it as a graphic designer, but I was finding it difficult to fit all the info into a digestible form. So I was going to do it in 3D and try to figure out how to convert it to a game environment that could be ported to web. AFAIK, it was just me doing what I could with PSCS2, AEP7, and a handful of 3D apps. What can you do? I don't know AI, flash or much to do with web design beyond simple html and maybe a little java script for specific tasks. So if you can do anything like that, I think we can get something done. Mind is the Defacto project manager.

I'm paid to do Linux multimedia programming (think of Netflix, Vudu, YouTube etc on your smart TV or Roku or WD live device). I did 2D game programming a few years back. We didn't use flash though, but lower level C++ engines. I know to use Photoshop for some semicom-plex tasks, but I'm not a pro, and I have never worked in Adobe Illustrator.

For this particular task, I can help by creating single elements (rectangles with text, signaling paths - arrows, etc...). I can help with project management too.

Speaking of managing the project, I think we should do the following:

• define clear project goals (requirements)
• agree upon the technology (the end format of the animation) we are going to use
• agree upon the tools
• evaluate the resources available (people and their skills)
• re-evaluate the project goals based on the available resources
• identify a task list and assign tasks to individuals
• track progress, identify issues and re-evaluate requirements based on them

Again, for this I recommend that we use trello as a tool that would help us with this. Everyone interested in this project should open a trello account and project manager (Mind) should create a project on trello and invite everyone interested.

But, the first step would be defining the project goals. Without clear target we are just aiming in the dark.

[Marios Kyriazis]

I am willing to support this project from the biological point of view, also expand it and include several other relevant areas. As mentioned, we need the copyright owner's permission and subsequent collaboration (I spoke to Dr M and is willing to take it further). This can be an interesting and important project that can raise awareness in biological aging and longevity.

[Andey]

I am willing to support this project from the biological point of view, also expand it and include several other relevant areas. As mentioned, we need the copyright owner's permission and subsequent collaboration (I spoke to Dr M and is willing to take it further). This can be an interesting and important project that can raise awareness in biological aging and longevity.

I am big fan of yours ) You write really interesting articles on longevity.
Glad you join us here )

[rikelme]

Few more proposals...

Hosting the source code
We'll have to host the source code (be it html + js, or actionscript if we decide to go with flash) and resources (images be it in png, svg, or any other format, sound effects, etc) of the animation somewhere. It is not good idea to keep everything on some private computer. The source and resources should be available publicly (write permissions will be given to active collaborators). There are several good choices out there, but github and bitbucket are by far the most popular ones. Both of them are completely free for open source projects, and beside source code versioning and hosting, they offer collaboration, project management and issue tracking too. We should decide which software versioning tool are we going to use. github supports git, whereas bitbucket support both git and mercurial. Personally, I prefer git.

Hosting the animation
We'll have to host the final animation somewhere. Again, there are many places where we can do it for free, but heroku is my favorite as it offers flawless integration with github and publishing a new version of the animation is just one command in console. What does heroku actually do for us? It keeps all the animation resources and people interested to see it it should just point their browser to the URL which would look something like: www.heroku.com/aging_biomarkers_schema. Of course, the application can be embedded into a random web page, including this websites page very easily.

All this probably sounds very technical to you guys who are not in software industry, but these are basic things that we need to decide on, if we want to finish this project.

Cheers !

Edited by Miroslav Ristić, 23 January 2013 - 12:19 AM.

[Andey]

Few more proposals...

Hosting the source code
We'll have to host the source code (be it html + js, or actionscript if we decide to go with flash) and resources (images be it in png, svg, or any other format, sound effects, etc) of the animation somewhere. It is not good idea to keep everything on some private computer. The source and resources should be available publicly (write permissions will be given to active collaborators). There are several good choices out there, but github and bitbucket are by far the most popular ones. Both of them are completely free for open source projects, and beside source code versioning and hosting, they offer collaboration, project management and issue tracking too. We should decide which software versioning tool are we going to use. github supports git, whereas bitbucket support both git and mercurial. Personally, I prefer git.

Hosting the animation
We'll have to host the final animation somewhere. Again, there are many places where we can do it for free, but heroku is my favorite as it offers flawless integration with github and publishing a new version of the animation is just one command in console. What does heroku actually do for us? It keeps all the animation resources and people interested to see it it should just point their browser to the URL which would look something like: www.heroku.com/aging_biomarkers_schema. Of course, the application can be embedded into a random web page, including this websites page very easily.

All this probably sounds very technical to you guys who are not in software industry, but these are basic things that we need to decide on, if we want to finish this project.

Cheers !

Totally agree with you about technical details ) I didnt familiar with web programming but get used to git at work.
I will look at Edge on weekend - its nice opportunity to learn something new.

I think that we have 2 different tasks here
1. First and main is about defining schema and relashionships itselfs. I think Dr Moskalev did a great job and give us good example how such schema could be done. With help of Marios Kyriazis and other respectfull professionals here we can extend schema and make it kind of crowdsourced document.
One option is to use some system modelling software like http://biologicalnetworks.net/, others is simplify it to some office diocuments. We need to ask forum medical and science professionals what tools they use or what kind of work process would be more suitable for them.
If we include resulted document to git repository than with (some instruction) non IT members could work on schema and relations, we could work on visualisation.

2 Second is technical and design, where we could participate by programming or desiging schema visualisation. It could be git+Edge+heroku as you propose.


And we still need some certanty with rights and final result - what we want to get at the end.

[okok]

We should ask ourselves what new we can contribute here. There's already a plethora of advanced tools out there - http://biologicalnetworks.net/ looks very interesting. Then again I've seen none specific to aging.

My suggestion is to concentrate on the presentation aspect - intuitive interactive graphics on the front end (edge, maybe d3 or the like) combined with a data driven imminst-crowd-sourced, preferably curated db backend. Dr. M's db should provide a nice starting point and if we can tie in or build upon aforementioned tools, all the better.

[rikelme]

We should ask ourselves what new we can contribute here. There's already a plethora of advanced tools out there - http://biologicalnetworks.net/ looks very interesting. Then again I've seen none specific to aging.

My suggestion is to concentrate on the presentation aspect - intuitive interactive graphics on the front end (edge, maybe d3 or the like) combined with a data driven imminst-crowd-sourced, preferably curated db backend. Dr. M's db should provide a nice starting point and if we can tie in or build upon aforementioned tools, all the better.

Completely agree. That is why i said that our first step should be: "define clear project goals (requirements)". Intuitive and eye candy visualization and animation is one of the primary things we should focus on.

I don't believe that we can or should compete with the "biological networks" application. Our focus should be strictly limited to one goal - creating the aging biomarkers schema interactive and easily expandable by non-tech users (crowd).

[Andey]

We should ask ourselves what new we can contribute here. There's already a plethora of advanced tools out there - http://biologicalnetworks.net/ looks very interesting. Then again I've seen none specific to aging.

My suggestion is to concentrate on the presentation aspect - intuitive interactive graphics on the front end (edge, maybe d3 or the like) combined with a data driven imminst-crowd-sourced, preferably curated db backend. Dr. M's db should provide a nice starting point and if we can tie in or build upon aforementioned tools, all the better.

I agree with datadriven mechanism.
I could start with translating dr Moskalev db to English, its definitely must to do work.

[okok]

I fetched the raw google translate into a db. I guess the next step would be to find a js graph layout algorithm and do the eye candy in edge (recursive sql for connection highlighting?).

Attached Files

•  BioMarkers.rar   36.91KB   8 downloads

[rikelme]

I fetched the raw google translate into a db. I guess the next step would be to find a js graph layout algorithm and do the eye candy in edge (recursive sql for connection highlighting?).

Hi Okok,

Thank you for the effort. As I can see, the DB you attached contains only biomarkers. There are no entries for Events, Aging-Dependent pathologies, and pathology markers which are all shown in the PDF. Do separate databases containing missing data exist?

We still have to decide what will be the use cases. For example, here are few:

• event: user clicks on a aging-dependent pathology; result: all related events appear
• event: user clicks on an event; result: all related biomarkers and pathologies appear with appropriate links
• etc...

Someone who has a clear vision how the animated schema should look and behave (most certainly including Dr Molaskev) should present the idea here, so we can start technical discussion how it can be done.

I think it would be great if you could export the data from the database in more human readable format (excel sheet) so non-technical participants can take a look as well. Shared google doc file should do.

Cheers!

[okok]

Thanks. It's more of a starting point, and the db doesn't match up 1:1 with the pdf - far as i can tell though, all the info should be in there.
Maybe Dr. Kyriazis wants to provide a schema/proof-reading? So long as we aren't content just converting the pdf, I thought along the lines of a wiki-like data model.

xls is here: https://docs.google....9wZWQxUXc#gid=0

[Mind]

I just wanted to point everyone to this current effort as well: http://www.denigma.de/ontology/graph

It is pretty much everything we could hope for, however, it definitely needs the "eye-candy" factor. The graphic is great however, we need it to be interactive and intuitive for non-tech people. I wonder if there is a way to make it 3-dimensional. It should have an expert/mode level and a more simplified level (a "gamified" version).

[Danail Bulgaria]

Is it possible also the opposite - the current state of the denigma ontology graph to be saved as a .jpg file

[Mind]

I'm offering to try to learn Edge. I was working on it as a graphic designer, but I was finding it difficult to fit all the info into a digestible form. So I was going to do it in 3D and try to figure out how to convert it to a game environment that could be ported to web. AFAIK, it was just me doing what I could with PSCS2, AEP7, and a handful of 3D apps. What can you do? I don't know AI, flash or much to do with web design beyond simple html and maybe a little java script for specific tasks. So if you can do anything like that, I think we can get something done. Mind is the Defacto project manager.

I'm paid to do Linux multimedia programming (think of Netflix, Vudu, YouTube etc on your smart TV or Roku or WD live device). I did 2D game programming a few years back. We didn't use flash though, but lower level C++ engines. I know to use Photoshop for some semicom-plex tasks, but I'm not a pro, and I have never worked in Adobe Illustrator.

For this particular task, I can help by creating single elements (rectangles with text, signaling paths - arrows, etc...). I can help with project management too.

Speaking of managing the project, I think we should do the following:

• define clear project goals (requirements)
  
• agree upon the technology (the end format of the animation) we are going to use
  
• agree upon the tools
  
• evaluate the resources available (people and their skills)
  
• re-evaluate the project goals based on the available resources
  
• identify a task list and assign tasks to individuals
  
• track progress, identify issues and re-evaluate requirements based on them

Again, for this I recommend that we use trello as a tool that would help us with this. Everyone interested in this project should open a trello account and project manager (Mind) should create a project on trello and invite everyone interested.

But, the first step would be defining the project goals. Without clear target we are just aiming in the dark.

Thanks for everyone for volunteering and the work you have done so far, getting things organized, offering suggestions (Andey, Okok, Miroslav, Marios, etc...) I had a meeting with some members of the ILA and the creator of the Denigma graph this weekend and we are basically starting to make a plan and define some goals, such as what Miroslav listed here. If anyone would like to join the group just let me know. We have tentatively scheduled weekly meetings for 12 GMT on Saturdays. I will also keep posting here to keep everyone in the loop.

[Danail Bulgaria]

Mind, do You mean, that You want to do something simmilar with the http://www.denigma.de/ontology/graph in 3d?

[Mind]

Mind, do You mean, that You want to do something simmilar with the http://www.denigma.de/ontology/graph in 3d?

Yes. In 3D and interactive. With different layers/levels that make it accessible to common people and scientists as well.

[Andey]

Mind, do You mean, that You want to do something simmilar with the http://www.denigma.de/ontology/graph in 3d?

Yes. In 3D and interactive. With different layers/levels that make it accessible to common people and scientists as well.

Good idea )
Only concern that it would be hard to implement it with volunteer team unless we could find good freeware visualisation script. May be hiring outsource sw development company would be more reliable choice for such big task.

[ilia]

This Saturday, at 12 GMT, there will be a skype chat dedicated to advancing the visualization project. If you are interested in participating, please pm me or mind your skype id, and we will be glad to add you to the chat (and development team).

[atraylen]

This is a neat project. I have no idea what would be best for a back end. However I do think that WebGl in conjunction with HTML5, CSS3 and Javascript (preferrably some library like jquery to handle interface behaviour) should be considered. As others did mention earlier flash is dead. Here are some links to some examples of implementations of webgl technologies...

• Planet To Web
• Zygote
• Globe Tutorial
• Khronos Demo Repository

The only real problem with this technology is the fact that users with slower systems or outdated or uncompatible browsers will be not be able to use a webgl implementation, however that does not mean once the data foundation is there that a less resource intensive.. or perhaps less graphically oriented representation of the data could be made available, if that seems to be something users are looking for.

[Mind]

If flash is dead, that is fine. I only mentioned it because that is what I am familiar with. Other graphical interface methods like atralyn mentioned look good as well. Whatever we can find that is familiar with project leaders/volunteers will work.

[rikelme]

If flash is dead, that is fine. I only mentioned it because that is what I am familiar with. Other graphical interface methods like atralyn mentioned look good as well. Whatever we can find that is familiar with project leaders/volunteers will work.

Flash isn't dead (look at all those Facebook games). It's popularity is declining, as well as portability (iOS doesn't support it). But, when it comes to writing web games it is still the first choice. Web apps that doesn't require such a high performance tend to be more developed in HTML5 recently (including the WebGL for real 3D applications, or just Javascript + CSS for 2D). I don't think that high performance is critical in our case. We don't have a lot of animations that have to be rendered at, say, 20 frames per second. Additionally, I don't think that we need real 3D support, or do we? When I say real 3D, I mean ability for a user to freely choose a perspective from which it will look at the object(s) we are presenting to him. So, WebGL is not a must. What we need, from what I understood after reading the first set of very general requirements, is to allow a user to toggle the visibility on/off of a certain layer on the graph. Each layer would represent another depth of complexity, or different kind of relations between certain elements on the graph. For this purpose plain 2D graphics with transparent layers which visibility can be turned ON or OFF will do.

As someone already pointed out, if the plan is to engage volunteers only, we should start off with realistic set of requirements, which would incrementally (in phases) add upon each other, in order to have a quick feedback and iterate fast. If, on the other hand, the plan is to hire professionals to finish the job, we have to have crystal clear set of requirements.

12 GMT, that is noon? If so, that is 3AM PST - not a good timing for me

It would be great if you could post a chat log here (or you can use http://pastebin.com/ - and just post link here).

Thanks,

Miro