MoHelmy commented 7 years ago

Developing a web interface for DoMo-Pred, the protein interactions prediction tool

Background

Protein-protein interactions (PPIs) are a central cellular activity that controls the function and behavior of the cells. They are either identified experimentally or predicted computationally. Many PPIs are mediated by protein modules that bind to small, linear protein sequence motifs that can be identified using high-throughput experiments followed by intensive computational analysis. Next, binding motif patterns can then be used to computationally PPIs mediated by them. DoMo-Pred is a command line tool that we recently developed. It uses protein linear motif identified high-throughput experimental for to scan the proteome for potential interactions with each motif and then filters these interaction using a range of evidence sources and cellular constraints on protein interactions using multiple Bayesian models. The current version of DoMo-Pred works for yeast proteins. Please read the following article for more details on DoMo-Pred.

Focus

The goal is to develop a web interface for the DoMo-Pred command line tool. This work could potentially lead to an independent publication or being part of the coming DoMo-Pred-Human paper.

Technology and Skills

DoMo-Pred command line tool is written in Python2.7 and C++. The student should have good command on these languages to understand the code. The student should have an excellent command of modern web technologies such as HTML5, CSS3, Django and/or others. The student will have the freedom to choose the technologies and languages to use as long as it is compatible with our web server.

Potential Mentors

Shobhit Jain, Mohamed Helmy, and Gary Bader (University of Toronto, Canada)

Contact

Interested students should contact: Shobhit Jain, Mohamed Helmy, Gary Bader

ankanch commented 7 years ago

Hello,

I don't have any prior experience with DoMo-Pred (I'd like to learn it). However, I have experience of using Python with Flask and HTML build websites and web APIs( like this ). Can I still apply for this project?

Thanks!

MoHelmy commented 7 years ago

Hi, Thanks for being interested in our project. This project does not require experience with Cityscape app. We evaluate candidate students based on a small task that helps us assess their suitability for the project. If you are willing to do the evaluation task (1 to 2 days task), please let us know. Thanks, Mohamed

On Jan 12, 2017, at 3:22 AM, hcnak notifications@github.com wrote:

Hello,

I don't have any prior experience with Cytoscape app. However, I have experience of using Python with Flask and HTML build websites and web APIs. Can I still apply for this project?

Thanks!

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub https://github.com/nrnb/GoogleSummerOfCode/issues/63#issuecomment-272102138, or mute the thread https://github.com/notifications/unsubscribe-auth/AHQkzM6bwgFXPzQiXnC6RzxRlMA0liJ5ks5rReK-gaJpZM4LDCyI.

ankanch commented 7 years ago

Thank you for replying me.

Yes,I'd like to do the evaluation task.So,when shall we start and should I do some preparation for it?

Thanks.

2017-01-13 2:42 GMT+08:00 Mohamed Helmy notifications@github.com:

Hi, Thanks for being interested in our project. This project does not require experience with Cityscape app. We evaluate candidate students based on a small task that helps us assess their suitability for the project. If you are willing to do the evaluation task (1 to 2 days task), please let us know. Thanks, Mohamed

========================= Mohamed Helmy, PhD Postdoc Researcher, Bader Lab The Donnelly Centre for Cellular and Biomolecular Research University of Toronto (UofT) individual.utoronto.ca/mohamedhelmy

On Jan 12, 2017, at 3:22 AM, hcnak notifications@github.com wrote:

Hello,

I don't have any prior experience with Cytoscape app. However, I have experience of using Python with Flask and HTML build websites and web APIs. Can I still apply for this project?

Thanks!

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub < https://github.com/nrnb/GoogleSummerOfCode/issues/63# issuecomment-272102138>, or mute the thread https://github.com/ notifications/unsubscribe-auth/AHQkzM6bwgFXPzQiXnC6RzxRlMA0li J5ks5rReK-gaJpZM4LDCyI.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/nrnb/GoogleSummerOfCode/issues/63#issuecomment-272245824, or mute the thread https://github.com/notifications/unsubscribe-auth/ADPo2GFRaYuv9GB1CXDNkUnJBnaCKTgzks5rRnQXgaJpZM4LDCyI .

-- Best regards,

Kanch http://akakanch.com ＠ Chengdu University of Information Technology 2015 Computer Science Major

Mail:kanchisme@gmail.com No.24 Block 1, Xuefu Road, Chengdu, Sichuan, China

MoHelmy commented 7 years ago

HI, Great, here is the description of the evaluation task that you need to do.

Task Description: Developing a simple web interface for the Yeast version of DoMo-Pred. The interface should perform the following functions: 1- Takes 2 protein IDs (or PWM and Domain files for simplicity). 2- Run DoMo-Pred analysis on the web server. 3- Returns the output in a table that is displayed in the web interface. These are the three major functions that the web interface for DoMo-Pred will perform (with several details that will be implemented in the actual project).

Tools and technologies: In principle, you are free to use the tools, languages or technologies that you feel comfortable using them. The modern web technologies should be used such HTML5, CSS3, JS and JQuery.

Timeline: The time for this task is 1~3 days.

Expected Deliverables: The developed prototype is expected to be hosted online so that we can access and evaluate the work. In case it is difficult to host the system online, you can send the work in one comprised file include all files required to run the system together with a detailed deployment guide.

Evaluation:

60 points for developing the three tasks.
10 points for delivering on time.
10 points for hosting the system online or sending it with detailed deployment guide.
10 points for code documentation and quality.
10 points for presentation (how good the look of the interface is). Bonus:
10 points for taking a list of pairs of protein IDs and returning their results.
10 points for fast delivery (finish in 1 day: +20 points, in 2 days: +10 points). Penalty:
Minus 5 points for delayed delivery (per day).

Resources: DoMo-Pred webpage http://baderlab.org/Software/DoMo-Pred http://baderlab.org/Software/DoMo-Pred DoMo-Pred paper http://baderlab.org/Publications?action=AttachFile&do=get&target=BioinfoFeb2016.pdf http://baderlab.org/Publications?action=AttachFile&do=get&target=BioinfoFeb2016.pdf DoMo-Pred paper supplementary materials http://baderlab.org/Software/DoMo-Pred?action=AttachFile&do=view&target=PRM_PPI_supplementary.pdf http://baderlab.org/Software/DoMo-Pred?action=AttachFile&do=view&target=PRM_PPI_supplementary.pdf A useful guide for developing biological web resources can be found in this article http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005128 and its list of resources and recommendations http://baderlab.org/TenRulesResources.

Please let us know if you have any questions. Best, Mohamed

On Jan 13, 2017, at 12:05 AM, hcnak notifications@github.com wrote:

Thank you for replying me.

Yes,I'd like to do the evaluation task.So,when will we start and should I do some preparation for it?

Thanks.

2017-01-13 2:42 GMT+08:00 Mohamed Helmy notifications@github.com:

Hi, Thanks for being interested in our project. This project does not require experience with Cityscape app. We evaluate candidate students based on a small task that helps us assess their suitability for the project. If you are willing to do the evaluation task (1 to 2 days task), please let us know. Thanks, Mohamed

========================= Mohamed Helmy, PhD Postdoc Researcher, Bader Lab The Donnelly Centre for Cellular and Biomolecular Research University of Toronto (UofT) individual.utoronto.ca/mohamedhelmy

On Jan 12, 2017, at 3:22 AM, hcnak notifications@github.com wrote:

Hello,

I don't have any prior experience with Cytoscape app. However, I have experience of using Python with Flask and HTML build websites and web APIs. Can I still apply for this project?

Thanks!

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub < https://github.com/nrnb/GoogleSummerOfCode/issues/63# issuecomment-272102138>, or mute the thread https://github.com/ notifications/unsubscribe-auth/AHQkzM6bwgFXPzQiXnC6RzxRlMA0li J5ks5rReK-gaJpZM4LDCyI.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/nrnb/GoogleSummerOfCode/issues/63#issuecomment-272245824, or mute the thread https://github.com/notifications/unsubscribe-auth/ADPo2GFRaYuv9GB1CXDNkUnJBnaCKTgzks5rRnQXgaJpZM4LDCyI .

-- Best regards,

Kanch http://akakanch.com ＠ Chengdu University of Information Technology 2015 Computer Science Major

Mail:kanchisme@gmail.com No.24 Block 1, Xuefu Road, Chengdu, Sichuan, China — You are receiving this because you were assigned. Reply to this email directly, view it on GitHub https://github.com/nrnb/GoogleSummerOfCode/issues/63#issuecomment-272362168, or mute the thread https://github.com/notifications/unsubscribe-auth/AHQkzKA3idrB0NGqBzSjx5_kSwXGyKJiks5rRwYggaJpZM4LDCyI.

ankanch commented 7 years ago

Hi, Thanks for giving me so detailed a task description.

I have downloaded the Yeast version of DoMo-Pred from http://baderlab.org/ , and set up the runtime environment , and then I have had executed the script several times. Knowing the input and output format. But I still have some questions.

For the first major function:

1- Takes 2 protein IDs (or PWM and Domain files for simplicity).

I have already know the PWM and Domain files, which in my task I think I should let user upload those files then analyze it (Is this right?).

As for Takes 2 protein IDs,I am a little confused about this,is this means user need only to input a so called protein ID, which is just a string,then DoMo-Pred will trying to analyze based on built-in data? Or , user still need to upload files contains the data used to analyze like files in pwm_dir folder of DoMo-Pred?

That's my only doubt, hope can be answered as soon , then I can start this evaluation.

Thanks a lot.

2017-01-13 23:11 GMT+08:00 Mohamed Helmy notifications@github.com:

HI, Great, here is the description of the evaluation task that you need to do.

Task Description: Developing a simple web interface for the Yeast version of DoMo-Pred. The interface should perform the following functions: 1- Takes 2 protein IDs (or PWM and Domain files for simplicity). 2- Run DoMo-Pred analysis on the web server. 3- Returns the output in a table that is displayed in the web interface. These are the three major functions that the web interface for DoMo-Pred will perform (with several details that will be implemented in the actual project).

Tools and technologies: In principle, you are free to use the tools, languages or technologies that you feel comfortable using them. The modern web technologies should be used such HTML5, CSS3, JS and JQuery.

Timeline: The time for this task is 1~3 days.

Expected Deliverables: The developed prototype is expected to be hosted online so that we can access and evaluate the work. In case it is difficult to host the system online, you can send the work in one comprised file include all files required to run the system together with a detailed deployment guide.

Evaluation:

60 points for developing the three tasks.

10 points for delivering on time.

10 points for hosting the system online or sending it with detailed deployment guide.

10 points for code documentation and quality.

10 points for presentation (how good the look of the interface is). Bonus:

10 points for taking a list of pairs of protein IDs and returning their results.

10 points for fast delivery (finish in 1 day: +20 points, in 2 days: +10 points). Penalty:

Minus 5 points for delayed delivery (per day).

Resources: DoMo-Pred webpage http://baderlab.org/Software/DoMo-Pred http://baderlab.org/Software/ DoMo-Pred DoMo-Pred paper http://baderlab.org/Publications?action=AttachFile&do=get&target= BioinfoFeb2016.pdf http://baderlab.org/Publications?action= AttachFile&do=get&target=BioinfoFeb2016.pdf DoMo-Pred paper supplementary materials http://baderlab.org/Software/DoMo-Pred?action=AttachFile& do=view&target=PRM_PPI_supplementary.pdf http://baderlab.org/Software/ DoMo-Pred?action=AttachFile&do=view&target=PRM_PPI_supplementary.pdf A useful guide for developing biological web resources can be found in this article http://journals.plos.org/ploscompbiol/article?id=10. 1371/journal.pcbi.1005128 and its list of resources and recommendations < http://baderlab.org/TenRulesResources>.

Please let us know if you have any questions. Best, Mohamed

On Jan 13, 2017, at 12:05 AM, hcnak notifications@github.com wrote:

Thank you for replying me.

Yes,I'd like to do the evaluation task.So,when will we start and should I do some preparation for it?

Thanks.

2017-01-13 2:42 GMT+08:00 Mohamed Helmy notifications@github.com:

Hi, Thanks for being interested in our project. This project does not require experience with Cityscape app. We evaluate candidate students based on a small task that helps us assess their suitability for the project. If you are willing to do the evaluation task (1 to 2 days task), please let us know. Thanks, Mohamed

========================= Mohamed Helmy, PhD Postdoc Researcher, Bader Lab The Donnelly Centre for Cellular and Biomolecular Research University of Toronto (UofT) individual.utoronto.ca/mohamedhelmy

On Jan 12, 2017, at 3:22 AM, hcnak notifications@github.com wrote:

Hello,

I don't have any prior experience with Cytoscape app. However, I have experience of using Python with Flask and HTML build websites and web APIs. Can I still apply for this project?

Thanks!

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub < https://github.com/nrnb/GoogleSummerOfCode/issues/63# issuecomment-272102138>, or mute the thread https://github.com/ notifications/unsubscribe-auth/AHQkzM6bwgFXPzQiXnC6RzxRlMA0li J5ks5rReK-gaJpZM4LDCyI.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/nrnb/GoogleSummerOfCode/issues/63# issuecomment-272245824, or mute the thread https://github.com/notifications/unsubscribe-auth/ ADPo2GFRaYuv9GB1CXDNkUnJBnaCKTgzks5rRnQXgaJpZM4LDCyI .

-- Best regards,

Kanch http://akakanch.com ＠ Chengdu University of Information Technology 2015 Computer Science Major

Mail:kanchisme@gmail.com No.24 Block 1, Xuefu Road, Chengdu, Sichuan, China — You are receiving this because you were assigned. Reply to this email directly, view it on GitHub < https://github.com/nrnb/GoogleSummerOfCode/issues/63# issuecomment-272362168>, or mute the thread https://github.com/ notifications/unsubscribe-auth/AHQkzKA3idrB0NGqBzSjx5_ kSwXGyKJiks5rRwYggaJpZM4LDCyI.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/nrnb/GoogleSummerOfCode/issues/63#issuecomment-272465926, or mute the thread https://github.com/notifications/unsubscribe-auth/ADPo2I6qi9_tXQgiGaNgjlVh_f5uNa2Kks5rR5Q1gaJpZM4LDCyI .

-- Best regards,

Kanch http://akakanch.com ＠ Chengdu University of Information Technology 2015 Computer Science Major

Mail:kanchisme@gmail.com No.24 Block 1, Xuefu Road, Chengdu, Sichuan, China

ankanch commented 7 years ago

Hi, I have tried a little. I'm not sure if this is what you what. I hosted it on my Amazon ECS. Hope you can take a look.

http://ec2-54-238-225-195.ap-northeast-1.compute.amazonaws.com:1996/

Just upload a pwm_file (not support folder yet) and a domain file , website will call DoMo-Pred then return the result. (it takes about 15 seconds)

I haven't render the result page yet. Just return the result directly. Result page will be like this: http://ec2-54-238-225-195.ap-northeast-1.compute.amazonaws.com:1996/result (haven't add table yet!)

I will render it later.

Hope this satisfy the requirements, so I can keep moving on.

Best, Long

MoHelmy commented 7 years ago

@ankanch 1- Yes, you are right. 2- Your description of "Takes 2 protein IDs" is correct. But for this task, let's keep it simple and just use the PWM and Domain.

MoHelmy commented 7 years ago

The prototype looks promising. Yes, you are in the correct direction. Please continue and let me know when you are done. I also suggest that you add a link to a PWM and domain files for download, so that when it comes to the evaluation, mentors from other projects can easily evaluate your work. They are not familiar with DoMo-Pred like us.

ankanch commented 7 years ago

@MoHelmy Thanks for you suggestion and review. By saying "let's keep it simple and just use the PWM and Domain." you mean to use those protein IDs in pwm_dir folder at current ?（ There will be a lot of protein IDs in actual project?）

Then I am keep moving on,thank you very much for your guidance.

MoHelmy commented 7 years ago

@ankanch Wahy I meant is "do exactly what you are doing, upload a PWM and a Domain file".

ankanch commented 7 years ago

@MoHelmy

Oh,sorry for misunderstanding. :) I'll continue the current work. ^_^

ankanch commented 7 years ago

Hi,

I think I may have finished the task. Although, I am still working on process multi-files( this works satisfied now,but the result page need to change a lot, I'm working on how to display the results and download multi-PWM file at the same time.)

However, I wish I can be evaluate now due to I will not be at home next week,because it's in vacation for chinese college students at this time.I will continue my work next weekend when I come back home.

At current, I have had rendered the result page. And raw PWM file can be download now as well as the domain files. In addition, you can get a permalink(here is a test permalink for P38822-2) of a result then share it .

As your suggestion, a link have been added for download test dataset.

I hope this satisfy the requirements . You can still evaluate it via link below: http://ec2-54-238-225-195.ap-northeast-1.compute.amazonaws.com:1996/

Thanks a lot. .

MoHelmy commented 7 years ago

Hi Long, Great work. This is exactly what we expect from a GSoC student. We cannot give a final acceptance/rejection now according to GSoC regulations. However, we can support your application and make you the primary candidate to this project. Your work indicated that you have what we need and that you quickly understood the concepts needed for the project. Please keep on tough and prepare your proposal so that we can help improving it before the submission time. Thanks very much. Mohamed

On Sun, Jan 15, 2017 at 9:48 AM hcnak notifications@github.com wrote:

Hi,

I think I may have finished. Although I am still working on process multi-files( this can work satisfied now,but the result page need to change a lot, I'm working on how to display the results and download multi-PWM file at the same time.)

However, I wish I can be evaluate now due to I will not be at home next week,because it's in vacation for chinese college students at this time.

At current, I have had render the result page. And raw PWM fiel can be download now as well as the domain files. In addition, you can get a permalink(here is a test permalink for P38822-2 http://ec2-54-238-225-195.ap-northeast-1.compute.amazonaws.com:1996/result/2017_01_15_14_47_20P38822-2) of a result and share it .

As your suggestion, a link have been added for download test dataset.

I hope this satisfy the requirements . You can still evaluate it via link below: http://ec2-54-238-225-195.ap-northeast-1.compute.amazonaws.com:1996/

Thanks a lot. .

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/nrnb/GoogleSummerOfCode/issues/63#issuecomment-272699810, or mute the thread https://github.com/notifications/unsubscribe-auth/AHQkzMxmC6KZzGOiZL26a45k4WfmC8Kfks5rSjHLgaJpZM4LDCyI .

ankanch commented 7 years ago

Hi,

Thank you so much.I'll keep moving on when I come back home,also, get my proposal ready as soon as possible.

Best, Long

2017-01-17 15:30 GMT+08:00 Mohamed Helmy notifications@github.com:

Hi Long, Great work. This is exactly what we expect from a GSoC student. We cannot give a final acceptance/rejection now according to GSoC regulations. However, we can support your application and make you the primary candidate to this project. Your work indicated that you have what we need and that you quickly understood the concepts needed for the project. Please keep on tough and prepare your proposal so that we can help improving it before the submission time. Thanks very much. Mohamed

On Sun, Jan 15, 2017 at 9:48 AM hcnak notifications@github.com wrote:

Hi,

I think I may have finished. Although I am still working on process multi-files( this can work satisfied now,but the result page need to change a lot, I'm working on how to display the results and download multi-PWM file at the same time.)

However, I wish I can be evaluate now due to I will not be at home next week,because it's in vacation for chinese college students at this time.

At current, I have had render the result page. And raw PWM fiel can be download now as well as the domain files. In addition, you can get a permalink(here is a test permalink for P38822-2 http://ec2-54-238-225-195.ap-northeast-1.compute.amazonaws. com:1996/result/2017_01_15_14_47_20P38822-2) of a result and share it .

As your suggestion, a link have been added for download test dataset.

I hope this satisfy the requirements . You can still evaluate it via link below: http://ec2-54-238-225-195.ap-northeast-1.compute.amazonaws.com:1996/

Thanks a lot. .

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/nrnb/GoogleSummerOfCode/issues/63# issuecomment-272699810, or mute the thread https://github.com/notifications/unsubscribe-auth/ AHQkzMxmC6KZzGOiZL26a45k4WfmC8Kfks5rSjHLgaJpZM4LDCyI .

--

Mohamed Helmy, PhD Postdoctoral Researcher, Bader Lab The Donnelly Centre University of Toronto individual.utoronto.ca/mohamedhelmy/

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/nrnb/GoogleSummerOfCode/issues/63#issuecomment-273041302, or mute the thread https://github.com/notifications/unsubscribe-auth/ADPo2CDvnQo2MU1rDALZEBqQF8MJbephks5rTG36gaJpZM4LDCyI .

-- Best regards,

Kanch http://akakanch.com ＠ Chengdu University of Information Technology 2015 Computer Science Major

Mail:kanchisme@gmail.com No.24 Block 1, Xuefu Road, Chengdu, Sichuan, China

MoHelmy commented 7 years ago

Hi Long, That seems great, I will check it later and come back to you. Please work on your proposal and let me know if you need help preparing it (e.g. something that is unclear in the task description). Thanks, Mohamed

On Mon, Jan 23, 2017 at 9:15 PM hcnak notifications@github.com wrote:

Hi,

I recently refine the evaluation task. The prototype can now process a list of PWM files and returning their results. Just press different buttons it will show different result for certain PWM file.

Best, Long

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/nrnb/GoogleSummerOfCode/issues/63#issuecomment-274681382, or mute the thread https://github.com/notifications/unsubscribe-auth/AHQkzESXElxMPX2O-1YmWU7MmNp7U-9Oks5rVV7JgaJpZM4LDCyI .

--

ankanch commented 7 years ago

Hi,

I have test it several times. It will always meet memory errors when the file is more than one due to the small memory of ECS2 (it will cost almost 600MB to analyze one file).

I just pinned a result image when process multi-files on my local machine below. When process multi-files , user can click buttons circled out in picture below to show different result.

By the way, I am still trying to reduce the memory cost and working on my proposal.

screenshot-127 0 0 1 5000-2017-01-24-11-44-26

Best, Long

MoHelmy commented 7 years ago

Great, thanks for the update. This is a very important point, I mean the memory problem, as we will face significant increase in the data size when we work with the human version of DoMo. It will be 8 to 10 GB. M

On Mon, Jan 23, 2017 at 10:55 PM hcnak notifications@github.com wrote:

Hi,

I have test it several times. It will always meet memory errors when the file is more than one due to the small memory of ECS2 (it will cost almost 600MB to analyze one file).

I just pinned a result image when process multi-files on my local machine below. When process multi-files , user can click buttons circled out in picture below to show different result.

By the way, I am still trying to reduce the memory cost and working on my proposal.

[image: screenshot-127 0 0 1 5000-2017-01-24-11-44-26] https://cloud.githubusercontent.com/assets/3401944/22233459/4b81c9f0-e22b-11e6-9123-8a3d691995ad.png

Best, Long

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/nrnb/GoogleSummerOfCode/issues/63#issuecomment-274698967, or mute the thread https://github.com/notifications/unsubscribe-auth/AHQkzFdHwJ6BpJVDPu_Iz_Q8tRaQx-Nuks5rVXYhgaJpZM4LDCyI .

--

ankanch commented 7 years ago

Hi, Memory problem is a little tricky here. I think there might be some optimizations should be applied to DoMo-Pred to reduce the memory cost. I'am still working on this point.

Besides, I need more information to prepare my proposal, I mean in actual project. My proposal now is writing depends on the idea description and evaluation task description. I wonder except upload PWM files( either one or more) then call DoMo-Pred to analyze it is there anything else should I do?

Best, Long

MoHelmy commented 7 years ago

The actual input will be the IDs of 2 proteins (or a list of pairs of IDs) and the domain and peptides info will be optional. DoMo used several types of info to assess the likelihood of interaction. Those will be listed and selectable (user can select which type of data to be used for the assessment). You can draft your proposal now with this info and later on we can improve it.

ankanch commented 7 years ago

Hi,

Thanks for your explanation。 I have sending a draft proposal to your email. Waiting for your reply. And I may come up a way to solve the memory problem. I'm going to apply it as soon as possible.

Thanks a lot.

MoHelmy commented 7 years ago

@ankanch The Proposal looks very good. Let's wait until GSoC officially stars and work more on it.

ankanch commented 7 years ago

Thank you so much.

ankanch commented 7 years ago

Hi,

Google had announced the organizations recently, what should I do then? Should I keep waiting until official student apply start?

Thanks.

MoHelmy commented 7 years ago

Ya, Google announced this yesterday. We got accepted. next is to improve your proposal and be ready for students application (I think this will be the last week of March).

MoHelmy commented 7 years ago

@ankanch Are you still interested in doing the project? If yes, please let me know as soon as possible. We need to finalize the proposal and make sure your prototype is online and working.

ankanch commented 7 years ago

Yes,I am still interested in doing this project.

And I will make my prototype online and working again in a few days .

Thank you.

2017-03-06 21:30 GMT+08:00 Mohamed Helmy notifications@github.com:

@ankanch https://github.com/ankanch Are you still interested in doing the project? If yes, please let me know as soon as possible. We need to finalize the proposal and make sure your prototype is online and working.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/nrnb/GoogleSummerOfCode/issues/63#issuecomment-284395938, or mute the thread https://github.com/notifications/unsubscribe-auth/ADPo2JdJYgyNbMN-4EtnfrQeWfRdC7Amks5rjAp_gaJpZM4LDCyI .

-- Best regards,

Long Zhang (Kanch) http://akakanch.com ＠ Chengdu University of Information Technology 2015 Computer Science Major

Mail:kanchisme@gmail.com No.24 Block 1, Xuefu Road, Chengdu, Sichuan, China

MoHelmy commented 7 years ago

Great, good to know.

On Mar 6, 2017, at 9:40 AM, hcnak notifications@github.com wrote:

Yes,I am still interested in doing this project.

And I will make my prototype online and working again in a few days .

Thank you.

2017-03-06 21:30 GMT+08:00 Mohamed Helmy notifications@github.com:

@ankanch https://github.com/ankanch Are you still interested in doing the project? If yes, please let me know as soon as possible. We need to finalize the proposal and make sure your prototype is online and working.

― You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/nrnb/GoogleSummerOfCode/issues/63#issuecomment-284395938, or mute the thread https://github.com/notifications/unsubscribe-auth/ADPo2JdJYgyNbMN-4EtnfrQeWfRdC7Amks5rjAp_gaJpZM4LDCyI .

-- Best regards,

Long Zhang (Kanch) http://akakanch.com ＠ Chengdu University of Information Technology 2015 Computer Science Major

Mail:kanchisme@gmail.com No.24 Block 1, Xuefu Road, Chengdu, Sichuan, China ― You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

ankanch commented 7 years ago

Hi,

I have been made my prototype online again. It has been migrated from Amazon ECS to the Digital Ocean, therefore,the memory problems now has been solved.

I have just refined it. Now you can use built-in domain file and just upload the PWM-files to analyze. In addition, all the source files and result files can be downloaded in a single zip file correctly when processing multi-files. And the permalink works as expected now.

I just did a test to analyze 6 PWM-files it cost 2 minutes with 800MB memory cost on average.(Click to see the result via permalink)

You can take a look of the prototype by clicking here.

And I will keep improving my proposal in the days after.

Thank you.

MoHelmy commented 7 years ago

Sounds great, I will check and come back to you. Please work in the proposal as well.

On Mar 8, 2017, at 8:36 AM, hcnak notifications@github.com wrote:

Hi,

I have been made my prototype online again. It has been migrated from Amazon ECS to the Digital Ocean, therefore,the memory problems now has been solved.

I have just refined it. Now you can use built-in domain file and just upload the PWM-files to analyze. In addition, all the source files and result files can be downloaded in a single zip file correctly when processing multi-files. And the permalink works as expected now.

I just did a test to analyze 6 PWM-files it cost 2 minutes with 800MB memory cost on average.(Click to see the result via permalink)

You can take a look of the prototype by clicking here.

And I will keep improving my proposal in the days after.

Thank you.

― You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

ankanch commented 7 years ago

Okay, thank you so much.

2017-03-08 22:06 GMT+08:00 Mohamed Helmy notifications@github.com:

Sounds great, I will check and come back to you. Please work in the proposal as well.

On Mar 8, 2017, at 8:36 AM, hcnak notifications@github.com wrote:

Hi,

I have been made my prototype online again. It has been migrated from Amazon ECS to the Digital Ocean, therefore,the memory problems now has been solved.

I have just refined it. Now you can use built-in domain file and just upload the PWM-files to analyze. In addition, all the source files and result files can be downloaded in a single zip file correctly when processing multi-files. And the permalink works as expected now.

I just did a test to analyze 6 PWM-files it cost 2 minutes with 800MB memory cost on average.(Click to see the result via permalink)

You can take a look of the prototype by clicking here.

And I will keep improving my proposal in the days after.

Thank you.

― You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/nrnb/GoogleSummerOfCode/issues/63#issuecomment-285049108, or mute the thread https://github.com/notifications/unsubscribe-auth/ADPo2CFlVtl-f91vOvnGxhgvZSqarK3Kks5rjrXNgaJpZM4LDCyI .

-- Best regards,

Long Zhang (Kanch) http://akakanch.com ＠ Chengdu University of Information Technology 2015 Computer Science Major

Mail:kanchisme@gmail.com No.24 Block 1, Xuefu Road, Chengdu, Sichuan, China

MoHelmy commented 7 years ago

Hi Long, I tried to open the 2 links but they seem to be broken. Please check and resend.

ankanch commented 7 years ago

I'm sorry,I found this error.I guess it is due to the DNS cache not refreshed yet.

Try visit the IP address directly will works fine.

http://138.68.4.76:1996/

Sorry for the inconvenience.

MoHelmy commented 7 years ago

Awesome, it works. Thanks.

On Wed, Mar 8, 2017 at 7:33 PM hcnak notifications@github.com wrote:

I'm sorry,I found this error.I guess it is due to the DNS cache not refreshed yet.

Try visit the IP address directly will works fine.

http://138.68.4.76:1996/

Sorry for the inconvenience.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/nrnb/GoogleSummerOfCode/issues/63#issuecomment-285216246, or mute the thread https://github.com/notifications/unsubscribe-auth/AHQkzPTVsGT6ff07yv8YPmOqqYzGZgYDks5rj0jogaJpZM4LDCyI .

--

Mohamed Helmy, PhD Postdoctoral Researcher, Bader Lab The Donnelly Centre University of Toronto individual.utoronto.ca/mohamedhelmy/

ankanch commented 7 years ago

Hi,

I have uploaded my draft proposal to GSOC site,looking forward to comments.I think my proposal may still need to be improved.

Thank you.

khanspers commented 7 years ago

GSoC 2017 selected project

nrnb / GoogleSummerOfCode