eQuilibrator Users

Contact owners and managers

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Welcome to the eQuilibrator Users support forum!

This is the place to post questions, report bugs, and discuss scientifically relevant issues relating to the online version of eQuilibrator.

In case you want to report bugs in equilibrator-api, please do so through the GitLab interface or send an email to this address.

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Oren yishai, Elad Noor2

May 1

Bug with displayed metabolite names in reactions

Hi Oren, thanks a lot for reporting this. I think I understand what the bug is. Anyhow, to avoid it

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Bug with displayed metabolite names in reactions

Hi Oren, thanks a lot for reporting this. I think I understand what the bug is. Anyhow, to avoid it

May 1

Yuxiang Hong

Mar 26

Why ΔrG'm and ΔrG'O remains the same in my reaction?

Hi, I am calculating the ΔrG'm and ΔrG'O for my reaction, and I found that ΔrG'm and ΔrG

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Why ΔrG'm and ΔrG'O remains the same in my reaction?

Hi, I am calculating the ΔrG'm and ΔrG'O for my reaction, and I found that ΔrG'm and ΔrG

Mar 26

Elisabeth Bubna-Litic, … James Sturgis6

Mar 15

Local cache - cxcalc license?

I too would be very interested in a workaround that avoids requiring a cxcalc licence... On Monday,

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Local cache - cxcalc license?

I too would be very interested in a workaround that avoids requiring a cxcalc licence... On Monday,

Mar 15

Robert Giessmann, Elad Noor2

Feb 20

eQuilibrator currently unavailable

Thanks to Robert for reporting the problem. It seems to be working again now, but I can't be sure

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eQuilibrator currently unavailable

Thanks to Robert for reporting the problem. It seems to be working again now, but I can't be sure

Feb 20

Ben, Elad Noor2

Jan 27

Compounds not present in KEGG

Hi Ben, I'm sorry I somehow missed this. Yes, there is a way to do it but it's a bit

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Compounds not present in KEGG

Hi Ben, I'm sorry I somehow missed this. Yes, there is a way to do it but it's a bit

Jan 27

Henry Leo, Elad Noor2

Jan 27

dG different between website and api

Hi Henry, I am sorry that I missed your question for such a long time. The answer is that on the

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dG different between website and api

Hi Henry, I am sorry that I missed your question for such a long time. The answer is that on the

Jan 27

Robert Giessmann

11/9/23

Participate in a Hackathon / Curate-athon on December 11th to 15th

Dear fellow eQuilibrator users, I would like to invite you to participate in a hackathon. You are

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Participate in a Hackathon / Curate-athon on December 11th to 15th

Dear fellow eQuilibrator users, I would like to invite you to participate in a hackathon. You are

11/9/23

Dan Olson, Elad Noor3

11/4/23

original_standard_dg_prime vs. standard_dg_prime

Hello Dan, to answer your the first question: the "original_standard_dg_prime" column

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original_standard_dg_prime vs. standard_dg_prime

Hello Dan, to answer your the first question: the "original_standard_dg_prime" column

11/4/23

Nathan Lamarre-Vincent, … Elad Noor7

11/1/23

Equilibrator still down?

Hi Eline, this is strange. Can you please provide more details such as: OS version python version are

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Equilibrator still down?

Hi Eline, this is strange. Can you please provide more details such as: OS version python version are

11/1/23

Eline De Lorenzo, Elad Noor2

10/4/23

eQuilibrator down?

Thanks Eline for letting us know about the error. I rebooted the server and it seems to be working

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eQuilibrator down?

Thanks Eline for letting us know about the error. I rebooted the server and it seems to be working

10/4/23

Scott McCain, Robert Giessmann2

9/12/23

'oops... Something Went Wrong' Error for 1,3-beta-Glucan

Dear Scott, sorry for the long delay to follow-up on your question. I wanted to notify you asap that

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'oops... Something Went Wrong' Error for 1,3-beta-Glucan

Dear Scott, sorry for the long delay to follow-up on your question. I wanted to notify you asap that

9/12/23

SANKAR MAHESH R, Elad Noor2

8/19/23

Regarding representation of chemicals

In general, you do not need to care about the protonations at all for the equilibrator calculations.

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Regarding representation of chemicals

In general, you do not need to care about the protonations at all for the equilibrator calculations.

8/19/23

Elad Noor2

8/3/23

Announcing equilibrator-api v0.5.0

Hello again, I'm happy to announce that version 0.5.0 has now been deployed also on conda-forge:

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Announcing equilibrator-api v0.5.0

Hello again, I'm happy to announce that version 0.5.0 has now been deployed also on conda-forge:

8/3/23

4/23/23

Regarding pathway analysis (result figure)

Hi, I am trying to perform pathway analysis for my pathway of interest, and I obtained the result

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Regarding pathway analysis (result figure)

Hi, I am trying to perform pathway analysis for my pathway of interest, and I obtained the result

4/23/23

SANKAR MAHESH R, Elad Noor2

3/3/23

Regarding parsing error

Dear Sankar, I guess you are trying to write a reaction that uses molecular oxygen (O2). Indeed, the

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Regarding parsing error

Dear Sankar, I guess you are trying to write a reaction that uses molecular oxygen (O2). Indeed, the

3/3/23

songcan chen, Elad Noor2

12/17/22

dG0' calculation for a reaction

Hi Songcan, Sorry for missing your question for so long. I hope this is still somewhat relevant, so I

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dG0' calculation for a reaction

Hi Songcan, Sorry for missing your question for so long. I hope this is still somewhat relevant, so I

12/17/22

12/17/22

unread,

12/17/22

12/17/22

convention for commas in reactions

Hi, Please use Tab-separated values (.tsv) which should solve the problem. I tried it and it worked (

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convention for commas in reactions

Hi, Please use Tab-separated values (.tsv) which should solve the problem. I tried it and it worked (

12/17/22

Michael Thornton, Elad Noor2

12/17/22

Ionic strength in calculations

Hi Michael, Sorry for the very late response. The ionic strength is indeed going into the activity

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Ionic strength in calculations

Hi Michael, Sorry for the very late response. The ionic strength is indeed going into the activity

12/17/22

Gerbo, Elad Noor2

9/19/22

SBtab generation in the API

Hi German, A while ago I wrote a CLI version of this script: https://gitlab.com/equilibrator/

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SBtab generation in the API

Hi German, A while ago I wrote a CLI version of this script: https://gitlab.com/equilibrator/

9/19/22

David Hala, Elad Noor2

9/5/21

problem running ecoli_noor_2016 example in jupyter notebook

Hello David, I'm sorry for the late response. Which version of equilibrator-pathway do you have

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problem running ecoli_noor_2016 example in jupyter notebook

Hello David, I'm sorry for the late response. Which version of equilibrator-pathway do you have

9/5/21

Ransac, Elad Noor5

7/6/21

error for fumarate/succinate potential

your arguments seem correct to me and you have convinced me that the values of the books are probably

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error for fumarate/succinate potential

your arguments seem correct to me and you have convinced me that the values of the books are probably

7/6/21

E.N. Smith, Elad Noor2

6/8/21

microspecies distribution and formation energies

Hi Ed, Indeed, all the relevant information (obtained using ChemAxon) is stored in the equilibrator-

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microspecies distribution and formation energies

Hi Ed, Indeed, all the relevant information (obtained using ChemAxon) is stored in the equilibrator-

6/8/21

Ronan MT Fleming, Elad Noor2

3/17/21

external interface to the structural subgroup decomposition

Hi Ronan, Thank you and sorry for taking time to reply. I think that there are two different issues

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external interface to the structural subgroup decomposition

Hi Ronan, Thank you and sorry for taking time to reply. I think that there are two different issues

3/17/21

Elad Noor

11/22/20

Announcing equilibrator-api v0.4.0 and a new conda package

Dear eQuilibrator users, I am happy to announce that we now have released a conda package in addition

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Announcing equilibrator-api v0.4.0 and a new conda package

Dear eQuilibrator users, I am happy to announce that we now have released a conda package in addition

11/22/20

Xin Wang, Elad Noor2

10/26/20

eQuilibrator down?

Hi Xin, Thanks for drawing my attention to it. I just restarted the server and it seems to be working

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eQuilibrator down?

Hi Xin, Thanks for drawing my attention to it. I just restarted the server and it seems to be working

10/26/20

kevinsh...@u.northwestern.edu, Elad Noor2

9/18/20

∆G formation of ubiquinol/one

Hi Kevin, Indeed reaction 1 uses direct information about the reduction potential of ubiquinol (

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∆G formation of ubiquinol/one

Hi Kevin, Indeed reaction 1 uses direct information about the reduction potential of ubiquinol (

9/18/20

Kevin Shebek, Elad Noor19

9/3/20

On-the-fly calculation of arbitrary compounds

Hi Kevin, Thank you for making the pull request. I think you made a very elegant solution and it

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On-the-fly calculation of arbitrary compounds

Hi Kevin, Thank you for making the pull request. I think you made a very elegant solution and it

9/3/20

Elad Noor

9/3/20

Announcement

Version 0.3.2 released

Dear eQuilibrator users, I'm happy to announce that version 0.3.2 of equilibrator-api has been

unread,

Announcement

Version 0.3.2 released

Dear eQuilibrator users, I'm happy to announce that version 0.3.2 of equilibrator-api has been

9/3/20

Daven Khana, … Elad Noor5

8/2/20

enzyme cost minimization variables

Great! Thanks again for the clarification. I've asked a bunch of questions on this group and have

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enzyme cost minimization variables

Great! Thanks again for the clarification. I've asked a bunch of questions on this group and have

8/2/20