Well done. I enjoyed your comparison between Poplar and Arabidopsis. However, I would have appreciated an phylogenetic tree and maybe some images of these plants for those unfamiliar with plant bio.
The wrapper was made due to CORS limitations, not quite the same as a firewall.
Amazing job on starting this app, especially for a beginner without any JavaScript experience!
For the inter-species comparison, I imagine you would allow users to choose their Arabidopsis Protein A and Poplar Protein A’. However, what if the Poplar has two orthologs to an Arabidopsis gene (due to an duplication event in Poplar). Could you imagine an auto-suggestion feature and how would you implement something like this? Hint… homolog/ortholog maps!
I like your project!
When the user selects high possibility or high-medium possibilty, what do these values represent? Would it be possible for the user to customize this (i.e. select exactly what threshold to use when highlighting amino acids?)
Also, I think the word “possibility” in those buttons should be “probability” (something being possible is different from something being probable)
Hey Wen Kai, I really enjoyed your presentation. Your walkthrough of the program really gave me an idea of what is happening, and I really appreciated the limitations/ next directions section. The double viewer feature seems to be very handy. You mentioned that the 3D mol rotation function isn’t always synchronous, do you have any idea why this may be?
Your presentation was very good! I thought you covered the background, reasoning and scope of your project very neatly!
I was wondering what other new features you think would be good to implement in the future. Also you mentioned that unrelated proteins don’t visualize well, but why is this a problem? What is the use case for visualizing SNPs for very different proteins?
Hi WenKai, Good work. I think if you introduced the goals of your tool and the applicability of visualizing SNPs, the presentation would flow better. For example, putting the ePlant slide before your tool slide. Good work expanding on your tool, highlighting the SOME of the new features. But you had some unmentioned features such as the tooltips (hover over AA residue) and your homolog search!
What protein did you highlight in chimera and did the associated homolog have a similar AA change?
If two proteins have similar AA mutations in a similar climate why do you think that would be? How would we visualize this on your app?
Thx, Vincent. I think I mentioned homolog button during demonstration. I should add more analysis about the proteins. I think same mutations in same climate may hint that the mutation can increase survival rate in that condition. AT5G11210.1 is the protein I used and there is no same position SNP change just similar region SNP change in the homolog so that AA change is a bit different. Additional docking analysis may require.
Great presentation. I really enjoyed the demonstration of SNPer, and you’ve done a good job implementing it. I think it looks quite powerful and I look forward to seeing how the data I helped provide will be integrated into it in the future.
The current interface for choosing what proteins to view seems to have some transparency issues on what is a valid or invalid input. For example, if the user forgets to specify they want to view a Poplar protein, the visualizer would not work. The drop-down menus I think could be a little confusing for the new user, especially if we look down a more distant future and more species are added to this cross-species viewer. I agree that user-centric design and accessibility is very important, so what improvements would you suggest to the module to address these difficulties?
Hi Luke, nice catch. Actually more than the find homolog button, there is autocomplete implemented the in input box so that user can pick one with the autocomplete. I forgot to mention that in the presentation. More over the input check will tell user what they did wrong with error which I didn’t demonstrate here but can be a good info to let user know what they do wrong. With more species implemented the input maybe input checked instead of using selection. For example, if the protein name start with a, it may be arabidopsis etc.
Excellent work! Walking though how to use the SNPer, really helped me understand the concepts. For the species, you later included Tomato as a close relative specie to Arabidopsis. However, you didn’t mention it at beginning. I wonder, why tomato can be a comparison specie to Arabidopsis and Poplar?
Hi Juliana, Tomato and Poplar can be inclusive because they ,as model species, have some databases with relatively high protein information. SNPer is just comparing the homolog of the proteins in different species. As long as the proteins in the species have homolog in other speceis, their nsSNPs can be compared. For example, the protein id AT5G01040.1 has homolog in many species Arabidopsis thaliana (Thale cress) Q9SR40-1 AT3G09220.1 such as
Arabidopsis thaliana (Thale cress) AT5G01050.1
Glycine max (Soybean) I1J744 GLYMA01G26750
Glycine max (Soybean) K7K337 GLYMA01G26800
Glycine max (Soybean) I1JLV8 GLYMA03G15800
Glycine max (Soybean) K7KDJ6 GLYMA03G15805
Glycine max (Soybean) I1KK82 GLYMA07G17140
Glycine max (Soybean) I1KK83 GLYMA07G17150
Glycine max (Soybean) I1KK85 GLYMA07G17170
Glycine max (Soybean) I1N2R2 GLYMA18G41860
Glycine max (Soybean) I1N2R3 GLYMA18G41870
Glycine max (Soybean) K7MTC5 GLYMA18G41886
Populus trichocarpa (Black Cottonwood) B9HC76 POPTR_0006S09520G
Populus trichocarpa (Black Cottonwood) U5FKZ9 POPTR_0016S099301G
Populus trichocarpa (Black Cottonwood) U5FNA6. All these proteins above can be compared in SNPer becasue they are homologs and have similar structures. In additon, poplar and arabidopsis are not close relative but similar proteins such as POPTR_0006S09520G and AT3G09220.1 can be compared. If they have similar location nsSNPs and due to similar stress, such nsSNP may help both species resist from the stress.
Hey Wen Kai,
Well done. I enjoyed your comparison between Poplar and Arabidopsis. However, I would have appreciated an phylogenetic tree and maybe some images of these plants for those unfamiliar with plant bio.
The wrapper was made due to CORS limitations, not quite the same as a firewall.
Amazing job on starting this app, especially for a beginner without any JavaScript experience!
For the inter-species comparison, I imagine you would allow users to choose their Arabidopsis Protein A and Poplar Protein A’. However, what if the Poplar has two orthologs to an Arabidopsis gene (due to an duplication event in Poplar). Could you imagine an auto-suggestion feature and how would you implement something like this? Hint… homolog/ortholog maps!
Blast the proteins and map them depend on similarity so that the more similar protein will be suggest first.
Hi Wen Kai,
I like your project!
When the user selects high possibility or high-medium possibilty, what do these values represent? Would it be possible for the user to customize this (i.e. select exactly what threshold to use when highlighting amino acids?)
Also, I think the word “possibility” in those buttons should be “probability” (something being possible is different from something being probable)
Hey Wen Kai, I really enjoyed your presentation. Your walkthrough of the program really gave me an idea of what is happening, and I really appreciated the limitations/ next directions section. The double viewer feature seems to be very handy. You mentioned that the 3D mol rotation function isn’t always synchronous, do you have any idea why this may be?
Hi Wen Kai,
Your presentation was very good! I thought you covered the background, reasoning and scope of your project very neatly!
I was wondering what other new features you think would be good to implement in the future. Also you mentioned that unrelated proteins don’t visualize well, but why is this a problem? What is the use case for visualizing SNPs for very different proteins?
Best,
Rachel
Hi WenKai, Good work. I think if you introduced the goals of your tool and the applicability of visualizing SNPs, the presentation would flow better. For example, putting the ePlant slide before your tool slide. Good work expanding on your tool, highlighting the SOME of the new features. But you had some unmentioned features such as the tooltips (hover over AA residue) and your homolog search!
What protein did you highlight in chimera and did the associated homolog have a similar AA change?
If two proteins have similar AA mutations in a similar climate why do you think that would be? How would we visualize this on your app?
Thx, Vincent. I think I mentioned homolog button during demonstration. I should add more analysis about the proteins. I think same mutations in same climate may hint that the mutation can increase survival rate in that condition. AT5G11210.1 is the protein I used and there is no same position SNP change just similar region SNP change in the homolog so that AA change is a bit different. Additional docking analysis may require.
Hi Wen Kai,
Great presentation. I really enjoyed the demonstration of SNPer, and you’ve done a good job implementing it. I think it looks quite powerful and I look forward to seeing how the data I helped provide will be integrated into it in the future.
The current interface for choosing what proteins to view seems to have some transparency issues on what is a valid or invalid input. For example, if the user forgets to specify they want to view a Poplar protein, the visualizer would not work. The drop-down menus I think could be a little confusing for the new user, especially if we look down a more distant future and more species are added to this cross-species viewer. I agree that user-centric design and accessibility is very important, so what improvements would you suggest to the module to address these difficulties?
Hi Luke, nice catch. Actually more than the find homolog button, there is autocomplete implemented the in input box so that user can pick one with the autocomplete. I forgot to mention that in the presentation. More over the input check will tell user what they did wrong with error which I didn’t demonstrate here but can be a good info to let user know what they do wrong. With more species implemented the input maybe input checked instead of using selection. For example, if the protein name start with a, it may be arabidopsis etc.
Hi! WenKai,
Excellent work! Walking though how to use the SNPer, really helped me understand the concepts. For the species, you later included Tomato as a close relative specie to Arabidopsis. However, you didn’t mention it at beginning. I wonder, why tomato can be a comparison specie to Arabidopsis and Poplar?
Hi Juliana, Tomato and Poplar can be inclusive because they ,as model species, have some databases with relatively high protein information. SNPer is just comparing the homolog of the proteins in different species. As long as the proteins in the species have homolog in other speceis, their nsSNPs can be compared. For example, the protein id AT5G01040.1 has homolog in many species Arabidopsis thaliana (Thale cress) Q9SR40-1 AT3G09220.1 such as
Arabidopsis thaliana (Thale cress) AT5G01050.1
Glycine max (Soybean) I1J744 GLYMA01G26750
Glycine max (Soybean) K7K337 GLYMA01G26800
Glycine max (Soybean) I1JLV8 GLYMA03G15800
Glycine max (Soybean) K7KDJ6 GLYMA03G15805
Glycine max (Soybean) I1KK82 GLYMA07G17140
Glycine max (Soybean) I1KK83 GLYMA07G17150
Glycine max (Soybean) I1KK85 GLYMA07G17170
Glycine max (Soybean) I1N2R2 GLYMA18G41860
Glycine max (Soybean) I1N2R3 GLYMA18G41870
Glycine max (Soybean) K7MTC5 GLYMA18G41886
Populus trichocarpa (Black Cottonwood) B9HC76 POPTR_0006S09520G
Populus trichocarpa (Black Cottonwood) U5FKZ9 POPTR_0016S099301G
Populus trichocarpa (Black Cottonwood) U5FNA6. All these proteins above can be compared in SNPer becasue they are homologs and have similar structures. In additon, poplar and arabidopsis are not close relative but similar proteins such as POPTR_0006S09520G and AT3G09220.1 can be compared. If they have similar location nsSNPs and due to similar stress, such nsSNP may help both species resist from the stress.