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GTU Systems Biology
Приєднався 18 жов 2020
This is the official channel of the Bioinformatics and Systems Biology Research Group at Gebze Technical University (GTU), Turkey.
Lecture 7.3 - Sampling based FBA | Genome Scale Metabolic Models
This is a 14-week course on Genome Scale Metabolic Models, taught by Tunahan Cakir at Gebze Technical University, TURKEY.
#SolutionSpace #ObjectiveFunction #Mammalian #HitAndRun
#SolutionSpace #ObjectiveFunction #Mammalian #HitAndRun
Переглядів: 705
Відео
Lecture 7.2 - Regulatory On Off Minimization (ROOM) | Genome Scale Metabolic Models
Переглядів 5223 роки тому
This is a 14-week course on Genome Scale Metabolic Models, taught by Tunahan Cakir at Gebze Technical University, TURKEY. #Optimization #MILP #KnockOut #MOMA #FBA #Metabolism
Lecture 7.1 - Minimization of Metabolic Adjustment (MOMA) | Genome Scale Metabolic Models
Переглядів 1,2 тис.3 роки тому
This is a 14-week course on Genome Scale Metabolic Models, taught by Tunahan Cakir at Gebze Technical University, TURKEY. #KnockOut #FBA #QuadraticProgramming
Lecture 6.3 - GUROBI Solver | Genome Scale Metabolic Models
Переглядів 6413 роки тому
This is a 14-week course on Genome Scale Metabolic Models, taught by Tunahan Cakir at Gebze Technical University, TURKEY. #Optimization #LinearProgramming #FBA
Lecture 6.4 - Overview of Yeast and Human Models | Genome Scale Metabolic Models
Переглядів 8483 роки тому
This is a 14-week course on Genome Scale Metabolic Models, taught by Tunahan Cakir at Gebze Technical University, TURKEY. #Recon #HMR #FBA
Lecture 6.2 - COBRA Toolbox | Genome Scale Metabolic Models
Переглядів 4,2 тис.3 роки тому
This is a 14-week course on Genome Scale Metabolic Models, taught by Tunahan Cakir at Gebze Technical University, TURKEY. #MATLAB #Metabolism #Flux
Lecture 6.1 - SBML Format | Genome Scale Metabolic Models
Переглядів 1,3 тис.3 роки тому
This is a 14-week course on Genome Scale Metabolic Models, taught by Tunahan Cakir at Gebze Technical University, TURKEY. #MetabolicNetwork #Flux #FBA
Lecture 5.5 - FBA Example: Nissen et al (1997) | Genome Scale Metabolic Models
Переглядів 4064 роки тому
This is a 14-week course on Genome Scale Metabolic Models, taught by Tunahan Cakir at Gebze Technical University, TURKEY. #FluxBalance #MetabolicNetwork #CarbonMole
Lecture 5.4 - GLPK Solver | Genome Scale Metabolic Models
Переглядів 1,2 тис.4 роки тому
This is a 14-week course on Genome Scale Metabolic Models, taught by Tunahan Cakir at Gebze Technical University, TURKEY. #LinearProgramming #FBA #Optimization
Lecture 5.3 - Minimization of Enzyme Usage | Genome Scale Metabolic Models
Переглядів 4914 роки тому
This is a 14-week course on Genome Scale Metabolic Models, taught by Tunahan Cakir at Gebze Technical University, TURKEY. #FBA #AlternateOptima #QuadraticProgramming
Lecture 5.2 - Flux Variability Analysis | Genome Scale Metabolic Models
Переглядів 1,1 тис.4 роки тому
This is a 14-week course on Genome Scale Metabolic Models, taught by Tunahan Cakir at Gebze Technical University, TURKEY. #FBA #FVA #AlternateOptima
Lecture 5.1 - Alternate Optima Definition | Genome Scale Metabolic Models
Переглядів 5614 роки тому
This is a 14-week course on Genome Scale Metabolic Models, taught by Tunahan Cakir at Gebze Technical University, TURKEY. #FluxBalance #FluxVariability #MetabolicNetworks
Lecture 4.3 - FBA Toy Example - Genome Scale Metabolic Models
Переглядів 7894 роки тому
This is a 14-week course on Genome Scale Metabolic Models, taught by Tunahan Cakir at Gebze Technical University, TURKEY. #FluxBalanceAnalysis #MetabolicNetwork #Optimization
Lecture 4.2 - Linear Programming | Genome Scale Metabolic Models
Переглядів 9314 роки тому
This is a 14-week course on Genome Scale Metabolic Models, taught by Tunahan Cakir at Gebze Technical University, TURKEY. #FluxBalanceAnalysis #Optimization #Constraints
Lecture 4.1 - Basics of Flux Balance Analysis | Genome Scale Metabolic Models
Переглядів 2,9 тис.4 роки тому
This is a 14-week course on Genome Scale Metabolic Models, taught by Tunahan Cakir at Gebze Technical University, TURKEY. #Underdetermined #linprog #ConstraintBasedAnalysis
Lecture 3.2 - Early Examples of Metabolic Flux Analysis | Genome Scale Metabolic Models
Переглядів 1,1 тис.4 роки тому
Lecture 3.2 - Early Examples of Metabolic Flux Analysis | Genome Scale Metabolic Models
Lecture 3.1 - Matrix Representation in MFA | Genome Scale Metabolic Models
Переглядів 2,3 тис.4 роки тому
Lecture 3.1 - Matrix Representation in MFA | Genome Scale Metabolic Models
Lecture 2.4 - Metabolic Flux Analysis (MFA) Class Exercise | Genome Scale Metabolic Models
Переглядів 1,6 тис.4 роки тому
Lecture 2.4 - Metabolic Flux Analysis (MFA) Class Exercise | Genome Scale Metabolic Models
Lecture 2.3 - Measurement of Extracellular Fluxes | Genome Scale Metabolic Models
Переглядів 8084 роки тому
Lecture 2.3 - Measurement of Extracellular Fluxes | Genome Scale Metabolic Models
Lecture 2.2 - Underdetermined Systems | Genome Scale Metabolic Models
Переглядів 9184 роки тому
Lecture 2.2 - Underdetermined Systems | Genome Scale Metabolic Models
Lecture 2.1 - Mass-balance Based Modelling | Genome Scale Metabolic Models
Переглядів 1,3 тис.4 роки тому
Lecture 2.1 - Mass-balance Based Modelling | Genome Scale Metabolic Models
Lecture 1.5 - ATP Requirements | Genome Scale Metabolic Models
Переглядів 8534 роки тому
Lecture 1.5 - ATP Requirements | Genome Scale Metabolic Models
Lecture 1.4 - Biomass Reaction | Genome Scale Metabolic Models
Переглядів 1,6 тис.4 роки тому
Lecture 1.4 - Biomass Reaction | Genome Scale Metabolic Models
Lecture 1.3 - Metabolic Precursors and Biosynthetic Pathways | Genome Scale Metabolic Models
Переглядів 1,8 тис.4 роки тому
Lecture 1.3 - Metabolic Precursors and Biosynthetic Pathways | Genome Scale Metabolic Models
Lecture 1.2 - Central Carbon Metabolism | Genome Scale Metabolic Models
Переглядів 2,5 тис.4 роки тому
Lecture 1.2 - Central Carbon Metabolism | Genome Scale Metabolic Models
Lecture 1.1 - Metabolic Networks | Genome Scale Metabolic Models
Переглядів 8 тис.4 роки тому
Lecture 1.1 - Metabolic Networks | Genome Scale Metabolic Models
Thank you! These are great lectures for beginners in GSMM like me.🙏
Aap video Hindi me translate krke bnaya kro plss
Kya hojayga agar aap Hindi me bologe 😭😭
I don't think prof. understand Hindi. He is from Türkiye.
I really like these videos. This is really great that you walk the audience through the history of these models and how they improved over time. Great job!
thank you!!!
Thanks for sharing. Your videos are very valuable!
Doctor thank you very muchhhh, Can't thank you enough i ve been searching for such materials for along time. Thank you, All the best for you.
The playlist is super helpful!!
Thank you so much for providing such good content. Are the slides available?
🙏🏻🙏🏻🙏🏻🙏🏻
Hi! Could you please share results of the exercise? It seems like the video that would go through them is missing! Thank you!
Hi! I @gtusysbio. I am enjoying the lectures! Could you please explain why do you include ATP, NADH and 02? Could the newtwork be written without them?
Is COBRA tool box still relevant today? Or should other tool box be preferred
Yes, COBRA is still the most functional tool out there for metabolic models. You can read the recent update on COBRA Toolbox from here: www.nature.com/articles/s41596-018-0098-2
Hi, Thank you for uploading the lectures, are very helpful to me! I wanted to ask you if you upload the slides?
Thank you. Indeed we are planning a github page where we will also share lecture slides, but it may take a couple of months.
that was really helpful, thanks a lot
Thank you very much for the explanation!
today i finished watching your all videos and they were very helpful to understand the subject. can you do a video on gene deletion and overexpression in E. coli and yeast using python based algorithm or any other algorithm. that would be of great help in further understanding the application of your lectures. thank you.
Thank you. We will include your suggestion in our to-do list. Thanks.
Thanks a lot for the course. Very helpful
Hi! I am really greatful for being able to see this course online. Excelent work and explanations Tunahan Cakir. I have a doubt about the quadratic optimization path (minimization of sum of squares of the internal fluxes) to minimize enzime usage: is there a reason or a notable advantage over the minimization of absolute sum of internal fluxes? Thank you.
Hi Matías. Thank you for your interest. There is no clear advantage of quadratic alternative (minimization of sum of squares) over linear alternative (minimization of absolute sum), or the other way around. If you use absolute sum, in a way, you assume a linear relation between flux and enzyme amount, which may look more logical. On the other hand, in a previous study of mine (doi.org/10.1039/C4MB00117F ) we saw a more significant correlation between the fluxes and transcriptome data when we used minimization of sum of squares. Of course, additional tests must be made to see if this is generalizable or not.
Thank you so much for your videos, I need to understand more about metabolic networks though I am not a metabolic engineer my research deals with metabolic models, trying to research an alternative algorithm for the optknock models
Hi, thanks for sharing, I learnt a lot from your video. Could you tell me where I can find the graph of pathway at 3:53? I read Lu's paper but didn't find it. Thanks.
Thank you. Please search for Roche Biochemical Pathways. www.roche.com/sustainability/philanthropy/science_education/pathways.htm
@@gtusysbio thank you very much.
Thank you for uploading this lecture series. I've just joined a metabolic modeling lab and this is a fantastic resource.
Thank you for the feedback!
Thank you for these lectures. I have followed them it has helped increase my knowledge on the subject. Is it possible to have hands-on workshop?
Thanks. Well, we have plans for this, but not soon.
I would be very interested to connect and learn more if there are other similar opportunities.
Thank you very much for these lectures. I have been searching for video lectures like this to help me with my research work. I am in Turkey as well, I would have loved to attend this program but it seems I am late.
I will also be working on Genome Scale Metabolic Modelling Sir any help would be much appreciated
Does it mean that as a synthetic biologist, one must be proficient in some programming language like MATLAB and Python. Is this assertion correct?
Hi, did you mean systems biologist? The popular languages are Python and R. When it comes to metabolic network modeling, Python and MATLAB are more popular, mostly because the famous COBRA Toolbox is available in both platform.
Your explanation is very explicit Sir. I am studying Bioengineering (MSc) at the University of Tartu, Estonia. I have immensely benefited from your online teaching. Thank you indeed.
At 6:40, how is did you get 10 rates (unknowns)? Please explain.
Sure, secretion of CO2 through the system boundary is another rate which is not depicted in the figure, making it 10.
Never mind, I have been able to figure it out.
@@gtusysbio Yes, I was able to figure that out from your explanation. Thank you very much.