Hosting Request for Circular Dichronism Spectroscopy - IIITH

sravanthimodepu commented 4 years ago

Hosting Details

The Request will be deployed on the infrastructure requested through the latest on-boarding request. Please raise an updated on-boarding request if extra resources are required for this hosting request.

Request Type:

[ ] Urgent
Note: All of the following request parameters are mandatory. Please do not remove or leave blank any fields.

Hosting Unit(Lab/Experiment) Name : Circular Dichronism Spectroscopy
Repo URL: https://github.com/virtual-labs/circular-dichronism-spectroscopy-iiith
Branch/Tag: master / v1.1
Contact Person: Sravanthi/Mrudhvika

Other Details

No

BalammaBoya commented 3 years ago

Hosting Details

The Request will be deployed on the infrastructure requested through the latest on-boarding request. Please raise an updated on-boarding request if extra resources are required for this hosting request.

Request Type:

[ ] Urgent
Note: All of the following request parameters are mandatory. Please do not remove or leave blank any fields.

Hosting Unit(Lab/Experiment) Name : Circular Dichronism Spectroscopy
Repo URL: https://github.com/virtual-labs/circular-dichronism-spectroscopy-iiith-js
Branch/Tag: master / v1.0.0
Contact Person: Balamma

Other Details

Note: This tag release is different repo from previous release repo , as we have created new repo with https://github.com/virtual-labs/circular-dichronism-spectroscopy-iiith-js for converting flash experiments to javascript experiment. So tag version started from v1.0.0 for new repo.

pavanchow commented 3 years ago

@BalammaBoya Add analytics code snippet to makefile and check request type.

BalammaBoya commented 3 years ago

@pavanchow Added analytics code snippet to makefile and released new tag.

Hosting Details

The Request will be deployed on the infrastructure requested through the latest on-boarding request. Please raise an updated on-boarding request if extra resources are required for this hosting request.

Request Type:

[ ] Urgent
Note: All of the following request parameters are mandatory. Please do not remove or leave blank any fields.

Hosting Unit(Lab/Experiment) Name : Circular Dichronism Spectroscopy
Repo URL: https://github.com/virtual-labs/circular-dichronism-spectroscopy-iiith-js
Branch/Tag: master / v1.1.0
Contact Person: Balamma

Other Details

No

pavanchow commented 3 years ago

Please add patch-analytics after all: help-dir in the makefile. By adding patch-analytics in all, you would be instructing the makefile to execute the code snippet present in patch-analytics.

You can refer the following makefile.

BalammaBoya commented 3 years ago

@pavanchow Updated make file with analytics code snippet to makefile and released new tag.

Hosting Details

The Request will be deployed on the infrastructure requested through the latest on-boarding request. Please raise an updated on-boarding request if extra resources are required for this hosting request.

Request Type:

[ ] Urgent
Note: All of the following request parameters are mandatory. Please do not remove or leave blank any fields.

Hosting Unit(Lab/Experiment) Name : Circular Dichronism Spectroscopy
Repo URL: https://github.com/virtual-labs/circular-dichronism-spectroscopy-iiith-js
Branch/Tag: master / v1.1.1
Contact Person: Balamma

Other Details

No

pavanchow commented 3 years ago

@BalammaBoya Repository size is 316.16 MiB and after building the lab, build(directory) size is more than 5 GB. Previous build(directory) size is 780 MB. Please fix this issue.

BalammaBoya commented 3 years ago

@pavanchow Reduced repo size and released new tag (v1.1.2 and v1.1.3).

Hosting Details

The Request will be deployed on the infrastructure requested through the latest on-boarding request. Please raise an updated on-boarding request if extra resources are required for this hosting request.

Request Type:

[ ] Urgent
Note: All of the following request parameters are mandatory. Please do not remove or leave blank any fields.

Hosting Unit(Lab/Experiment) Name : Circular Dichronism Spectroscopy
Repo URL: https://github.com/virtual-labs/circular-dichronism-spectroscopy-iiith-js
Branch/Tag: master / v1.1.2 and v1.1.3
Contact Person: Balamma

Other Details

No

pavanchow commented 3 years ago

@BalammaBoya

Hosted Circular Dichronism Spectroscopy lab. Hosted URL of Lab: http://cds-iiith.vlabs.ac.in Branch/Tag : master/v1.1.3

Please check and approve the same.

BalammaBoya commented 3 years ago

@pavanchow hosted source is working fine.

Screenshot from 2020-12-07 12-12-51

pavanchow commented 2 years ago

Issues:

Background principle page: broken link
Experiment 8: broken link in theory page
Experiment 9: broken link in theory page

sravanthimodepu commented 2 years ago

Repo Owner Details Name - Sravanthi GitHub handle - sravanthimodepu Email id - sravanthimodepu@vlabs.ac.in

Lab Name: Circular Dichroism Spectroscopy Lab

To determine the specific rotation of a sugar using a polarimeter - https://github.com/virtual-labs/exp-rotation-of-sugar-iiith
To understand the effect of chiral substances on plane polarized light as a function of wavelength - https://github.com/virtual-labs/exp-effect-chiral-substances-iiith
To study the Optical Rotatory Dispersion (ORD) of some chiral substances - https://github.com/virtual-labs/exp-optical-rotatory-dispersion-iiith
To study the Circular Dichroism of some substances with chiral chromophores - https://github.com/virtual-labs/exp-substances-with-chiral-chromophores-iiith
To Study the operational details of a CD spectrometer - https://github.com/virtual-labs/exp-cd-spectrometer-iiith
To Study the effect of Secondary Structure elements on CD spectrum of proteins - https://github.com/virtual-labs/exp-cd-spectrum-of-proteins-iiith
To deconvolute the CD spectrum of a given protein solution and to classify it in terms of its secondary structure elements - https://github.com/virtual-labs/exp-secondary-structure-elements-iiith
To study the thermal stability of proteins - https://github.com/virtual-labs/exp-thermal-stability-of-proteins-iiith
To study the effect of chemical denaturants on protein stability - https://github.com/virtual-labs/exp-chemical-denaturants-iiith
To study the comparison between protein unfolding and protein aggregation in the presence of chemical denaturing agents - https://github.com/virtual-labs/exp-chemical-denaturing-agents-iiith

Lab url: http://cds-iiith.vlabs.ac.in/

Introduction:

Circular dichroism (CD) spectroscopy is a spectroscopic technique where the CD of molecules is measured over a range of wavelengths. CD spectroscopy is used extensively to study chiral molecules of all types and sizes, but it is in the study of large biological molecules where it finds its most important applications. A primary use is in analyzing the secondary structure or conformation of macromolecules, particularly proteins, and because secondary structure is sensitive to its environment, e.g. temperature or pH, circular dichroism can be used to observe how secondary structure changes with environmental conditions or on interaction with other molecules. Structural, kinetic and thermodynamic information about macromolecules can be derived from circular dichroism spectroscopy.

Circular dichroism spectroscopy is particularly useful for:

Determining whether a protein is folded, and if so characterizing its secondary structure, tertiary structure, and the structural family to which it belongs
- Comparing the structures of a protein obtained from different sources (e.g. species or expression systems) or comparing structures for different mutants of the same protein
- Demonstrating comparability of solution conformation and/or thermal stability after changes in manufacturing processes or formulation
- Studying the conformational stability of a protein under stress -- thermal stability, pH stability, and stability to denaturants and how this stability is altered by buffer composition or addition of stabilizers and excipients
- CD is excellent for finding solvent conditions that increase the melting temperature and/or the reversibility of thermal unfolding, conditions which generally enhance shelf life
- Determining whether protein-protein or protein-ligand interactions alter the conformation of protein
- If there are any conformational changes, this will result in a spectrum which will differ from the sum of the individual components. Small conformational changes have been seen, for example, upon formation of several different receptor/ligand complexes

Objective:

To study chiral molecules of all types and sizes, but it is in the study of large biological molecules where it finds its most important applications.

Course Alignment: This virtual lab on Circular Dichroism Spectroscopy Lab is to be used as a supplement to a parallel course on the same topic. It is not designed to be a complete course/tutorial by itself where a student can learn Circular Dichroism Spectroscopy Lab just by going through the designed experiments.

Target Audience: Circular Dichroism Virtual Laboratory is desigen for mainly Under Graduate (3rd/4th year) and Post Graduate students. This lab will serve the purpose of interest of a large and diverse group of students.

Following students may be benefited from this lab.

Undergraduate (B.Tech, B.Sc.), Postgraduates (M.Sc, M.Pharm) as part of courses Biotechnology, Biochemistry, Chemistry.
Undergradute and post graduate level (M.S., diploma, and Ph.D level) as part of courses Biotechnology, Biochemical engineering, Biophysics, Structural Biophysics, Structural Molecular Biology, Molecular Biophysics.

This lab may also be helpful for research scientists interested in photochemistry and photobiology.

pavanchow commented 2 years ago

@BalammaBoya

Hosted Circular Dichronism Spectroscopy lab. Hosted URL of Lab: https://cds-iiith.vlabs.ac.in

Please check and approve the same.

BalammaBoya commented 2 years ago

@pavanchow : Experiment4 (To study the Circular Dichroism of some substances with chiral chromophores ) content is missing on production which is working on github pages. Could you please cross check. Please revert in to the old source.

Production screen short: Screenshot from 2021-09-30 23-27-19

Github pages screen short: Screenshot from 2021-09-30 23-28-29

BalammaBoya commented 2 years ago

Lab Name: Circular Dichroism Spectroscopy Lab

To determine the specific rotation of a sugar using a polarimeter - https://github.com/virtual-labs/exp-rotation-of-sugar-iiith | main | v1.0.0 |
To understand the effect of chiral substances on plane polarized light as a function of wavelength - https://github.com/virtual-labs/exp-effect-chiral-substances-iiith | main | v1.0.0 |
To study the Optical Rotatory Dispersion (ORD) of some chiral substances - https://github.com/virtual-labs/exp-optical-rotatory-dispersion-iiith | main | v1.0.0 |
To study the Circular Dichroism of some substances with chiral chromophores - https://github.com/virtual-labs/exp-substances-with-chiral-chromophores-iiith | main | v1.0.1|
To Study the operational details of a CD spectrometer - https://github.com/virtual-labs/exp-cd-spectrometer-iiith | main | v1.0.0|
To Study the effect of Secondary Structure elements on CD spectrum of proteins - https://github.com/virtual-labs/exp-cd-spectrum-of-proteins-iiith | main | v1.0.0|
To deconvolute the CD spectrum of a given protein solution and to classify it in terms of its secondary structure elements - https://github.com/virtual-labs/exp-secondary-structure-elements-iiith | main | v1.0.0 |
To study the thermal stability of proteins - https://github.com/virtual-labs/exp-thermal-stability-of-proteins-iiith | main |
To study the effect of chemical denaturants on protein stability - https://github.com/virtual-labs/exp-chemical-denaturants-iiith | main | v1.0.0|
To study the comparison between protein unfolding and protein aggregation in the presence of chemical denaturing agents - https://github.com/virtual-labs/exp-chemical-denaturing-agents-iiith | main | v1.0.0 |

Lab url: http://cds-iiith.vlabs.ac.in/

pavanchow commented 2 years ago

@BalammaBoya

Hosted Circular Dichronism Spectroscopy lab with "4. To study the Circular Dichroism of some substances with chiral chromophores" Hosted URL of Lab: https://cds-iiith.vlabs.ac.in

Please check and approve the same.

BalammaBoya commented 2 years ago

@pavanchow : Hosted source is working fine and It's Approved.

ravikiran2020 commented 1 month ago

Rehosting the lab with Bug Report and Rating Feature

virtual-labs / engineers-forum