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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Elad Noor, … Dan Olson9

11/16/18

Announcement

equilibrator-api is now available on PyPI

I'm not sure if I understand your question. The DataFrames are only created for facilitating the

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Announcement

equilibrator-api is now available on PyPI

I'm not sure if I understand your question. The DataFrames are only created for facilitating the

11/16/18

Dan Olson, … Elad Noor8

Apr 27

original_standard_dg_prime vs. standard_dg_prime

Hi, 1) Regarding the explanation about the constraints on the standard reaction ΔG's, I prefer

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original_standard_dg_prime vs. standard_dg_prime

Hi, 1) Regarding the explanation about the constraints on the standard reaction ΔG's, I prefer

Apr 27

Maggie Cook, Elad Noor2

Feb 5

cc.search_compound confidence metric?

Hello, Yes, search_compound is simply a wrapper for the CompoundCache function "search":

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cc.search_compound confidence metric?

Hello, Yes, search_compound is simply a wrapper for the CompoundCache function "search":

Feb 5

Jasmin Bauer, Elad Noor4

Jan 12

NAD/NADH reduction potential

Hi, Thanks for the reference, I didn't know about it. I think there might be a slight confusion

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NAD/NADH reduction potential

Hi, Thanks for the reference, I didn't know about it. I think there might be a slight confusion

Jan 12

Robert Giessmann

12/17/24

Invitation to hackathon in week of 2025-01-13 to improve data basis for eQuilibrator

Dear fellow eQuilibrator users, Are you enjoying the predictions of eQuilibrator? You can work with

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Invitation to hackathon in week of 2025-01-13 to improve data basis for eQuilibrator

Dear fellow eQuilibrator users, Are you enjoying the predictions of eQuilibrator? You can work with

12/17/24

Niels Hollmann, Elad Noor3

12/10/24

Equilibrator Web security certificate expired

Hopefully the certificate has been update and now things should work as normal. On Monday, December 9

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Equilibrator Web security certificate expired

Hopefully the certificate has been update and now things should work as normal. On Monday, December 9

12/10/24

Jackson Bland

11/20/24

Can't find 4-oxopentanoyl-CoA

For some reason no matter what identifier is used I can't get the api to recognize 4-oxopentanoyl

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Can't find 4-oxopentanoyl-CoA

For some reason no matter what identifier is used I can't get the api to recognize 4-oxopentanoyl

11/20/24

Gabe Rubinstein, Elad Noor2

9/22/24

How to cite?

Hello, Thank you for inquiring about how to cite our work. It depends a bit on which values you are

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How to cite?

Hello, Thank you for inquiring about how to cite our work. It depends a bit on which values you are

9/22/24

郁熹林, Elad Noor3

9/6/24

Activation eQuilibrator API problem after finishing installation

It seems that I managed to fix the conda packages, hopefully. You can try that if you haven't yet

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Activation eQuilibrator API problem after finishing installation

It seems that I managed to fix the conda packages, hopefully. You can try that if you haven't yet

9/6/24

Oren yishai, Elad Noor2

9/4/24

The compound Ethane is not available

It was probably missing from metanetx when we updated the database last time. Sorry, but it will

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The compound Ethane is not available

It was probably missing from metanetx when we updated the database last time. Sorry, but it will

9/4/24

Karel Olavarria, … Elad Noor5

8/6/24

calculations with eQuilibrator when solid compounds are involved

Hi Karel and thanks Robert for your input, Specifically for sulfur, we have an exception for having

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calculations with eQuilibrator when solid compounds are involved

Hi Karel and thanks Robert for your input, Specifically for sulfur, we have an exception for having

8/6/24

Robert Giessmann

7/28/24

Interest in co-hosting a hackathon?

Dear fellow eQuilibrator users, As you might know, eQuilibrator relies on experimental data and there

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Interest in co-hosting a hackathon?

Dear fellow eQuilibrator users, As you might know, eQuilibrator relies on experimental data and there

7/28/24

Robert Giessmann

5/22/24

Can you explain thermodynamics in 30 seconds?

Dear all, I am happy to share that openTECR, the open database on thermodynamics of enzyme-catalyzed

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Can you explain thermodynamics in 30 seconds?

Dear all, I am happy to share that openTECR, the open database on thermodynamics of enzyme-catalyzed

5/22/24

Oren yishai, Elad Noor3

5/3/24

Bug with displayed metabolite names in reactions

Okay, the bug has been patched. Now, having protons in the formula shouldn't cause any problems (

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Bug with displayed metabolite names in reactions

Okay, the bug has been patched. Now, having protons in the formula shouldn't cause any problems (

5/3/24

Yuxiang Hong

3/26/24

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

3/26/24

Elisabeth Bubna-Litic, … James Sturgis6

3/15/24

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,

3/15/24

Robert Giessmann, Elad Noor2

2/20/24

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

2/20/24

Ben, Elad Noor2

1/27/24

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

1/27/24

Henry Leo, Elad Noor2

1/27/24

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

1/27/24

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

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