Add sims and/or exps from previous NMRlipids papers

[comcon1]

We agreed that we should add the systems from the previous papers by NMRlipids Open Collaboration. We can make a list here and then tick the checkboxes.

[batukav]

I compared the DOIs in BilayerData and the other NMRLipids repositories, namely

https://github.com/NMRLipids/NMRlipidsVIpolarizableFFs
https://github.com/NMRLipids/NmrLipidsCholXray
https://github.com/NMRLipids/NmrLipidsCholXray
https://github.com/NMRLipids/MATCH
https://github.com/NMRLipids/NMRlipidsIVPEandPG
https://github.com/NMRLipids/lipid_ionINTERACTION
https://github.com/NMRLipids/NMRlipidsIVotherHGs

There are around 200 missing DOIs. Would comparing the DOIs be a reasonable test? Should I be looking into other possibilities?

[comcon1]

I compared the DOIs

Are you talking about Simulations or Experiments? For simulations, DOI is OK I think. Despite it's a different version of same Zenodo. That could make a collision. Otherwise it looks fine.

[batukav]

I mean simulations. Different versions of the same system is indeed a good observation. I will try to check that as well.

I don't have much experience with the experiments, I would be happy to hear your suggestions.

[comcon1]

I would be happy to hear your suggestions.

Experiments are always related to the paper, except in cases when they are without paper. If an experiment is done within a particular NMRlipids paper, then it can be the NMRlipids Paper's doi standing with this experiment. I think we can start by just opening draft PR related to one NMRlipids paper, which has data which is missing in the main repo, and then I will join and check something. Or some other will join.

[batukav]

Below is what I managed to find regarding the simulations so far.

Missing Zenodo DOIs in BilayerData

• Total unique DOIs in BilayerData: 469
• Total unique DOIs in satellite repos: 309
• Candidate missing (before version check): 108
• Truly missing (no version in BilayerData): 46
• Matched via version check: 62

All candidate DOIs and version status

missing full doi	multiple versions on Zenodo	matching version DOI on BilayerData
10.5281/zenodo.12652	false
10.5281/zenodo.12654	false
10.5281/zenodo.12743	false
10.5281/zenodo.13279	true	10.5281/zenodo.4643875
10.5281/zenodo.13281	true	10.5281/zenodo.4643914
10.5281/zenodo.13282	true	10.5281/zenodo.4643899
10.5281/zenodo.13283	true	10.5281/zenodo.4643985
10.5281/zenodo.13286	true	10.5281/zenodo.4644028
10.5281/zenodo.13392	false
10.5281/zenodo.13393	false
10.5281/zenodo.13791	true	10.5281/zenodo.5734452
10.5281/zenodo.13821	false
10.5281/zenodo.13877	true	10.5281/zenodo.3252052
10.5281/zenodo.13946	true	10.5281/zenodo.4740115
10.5281/zenodo.15548	true	10.5281/zenodo.6656031
10.5281/zenodo.16830	false
10.5281/zenodo.17004	false
10.5281/zenodo.17208	false
10.5281/zenodo.30904	false
10.5281/zenodo.32496	true	10.5281/zenodo.4750862
10.5281/zenodo.34415	false
10.5281/zenodo.55318	false
10.5281/zenodo.55322	false
10.5281/zenodo.57845	true
10.5281/zenodo.60607	true	10.5281/zenodo.3243328
10.5281/zenodo.61992	true	10.5281/zenodo.3238157
10.5281/zenodo.153947	false
10.5281/zenodo.154346	true	10.5281/zenodo.3243329
10.5281/zenodo.159759	true	10.5281/zenodo.3237420
10.5281/zenodo.167336	false
10.5281/zenodo.209070	false
10.5281/zenodo.209080	false
10.5281/zenodo.209381	false
10.5281/zenodo.209391	false
10.5281/zenodo.887397	true	10.5281/zenodo.887398
10.5281/zenodo.887399	true	10.5281/zenodo.887400
10.5281/zenodo.1011095	true	10.5281/zenodo.1011096
10.5281/zenodo.1011104	false
10.5281/zenodo.1120287	false
10.5281/zenodo.1129430	true	10.5281/zenodo.1129431
10.5281/zenodo.1129434	true	10.5281/zenodo.1129435
10.5281/zenodo.1134869	true
10.5281/zenodo.1135142	false
10.5281/zenodo.1148495	false
10.5281/zenodo.1167532	false
10.5281/zenodo.1210255	true
10.5281/zenodo.1210256	true
10.5281/zenodo.1227256	true
10.5281/zenodo.1227257	true
10.5281/zenodo.1227272	true
10.5281/zenodo.1230169	true	10.5281/zenodo.1230170
10.5281/zenodo.1250969	false
10.5281/zenodo.1250975	false
10.5281/zenodo.1283334	true	10.5281/zenodo.1283335
10.5281/zenodo.1288296	true	10.5281/zenodo.1288297
10.5281/zenodo.1293761	true	10.5281/zenodo.1293762
10.5281/zenodo.1293812	true	10.5281/zenodo.1293813
10.5281/zenodo.1293852	true
10.5281/zenodo.1293853	false
10.5281/zenodo.1293854	true
10.5281/zenodo.1293855	false
10.5281/zenodo.1293888	true	10.5281/zenodo.1293889
10.5281/zenodo.1293904	true	10.5281/zenodo.1293905
10.5281/zenodo.1293927	true	10.5281/zenodo.1293928
10.5281/zenodo.1293931	true	10.5281/zenodo.1293932
10.5281/zenodo.1293940	true	10.5281/zenodo.1293941
10.5281/zenodo.1293956	true	10.5281/zenodo.1293957
10.5281/zenodo.1306799	true	10.5281/zenodo.1306800
10.5281/zenodo.1306820	true	10.5281/zenodo.1306821
10.5281/zenodo.1319601	true
10.5281/zenodo.1404040	true
10.5281/zenodo.1409551	true
10.5281/zenodo.1434990	false
10.5281/zenodo.1475284	true	10.5281/zenodo.1475285
10.5281/zenodo.1487760	true	10.5281/zenodo.1487761
10.5281/zenodo.2532248	true	10.5281/zenodo.2542176
10.5281/zenodo.2532249	true	10.5281/zenodo.2542176
10.5281/zenodo.2542134	true	10.5281/zenodo.2542135
10.5281/zenodo.2542150	true	10.5281/zenodo.2542151
10.5281/zenodo.2542163	true	10.5281/zenodo.2542164
10.5281/zenodo.2572897	true	10.5281/zenodo.3378992
10.5281/zenodo.2573530	true	10.5281/zenodo.2573531
10.5281/zenodo.2573905	true	10.5281/zenodo.4386514
10.5281/zenodo.2574490	true	10.5281/zenodo.2574491
10.5281/zenodo.2574533	true	10.5281/zenodo.2578069
10.5281/zenodo.2577305	true	10.5281/zenodo.4424934
10.5281/zenodo.2579675	false
10.5281/zenodo.2633773	true	10.5281/zenodo.3269320
10.5281/zenodo.2641986	true	10.5281/zenodo.2641987
10.5281/zenodo.3378970	true	10.5281/zenodo.4424292
10.5281/zenodo.3474862	true	10.5281/zenodo.3474863
10.5281/zenodo.3483784	true	10.5281/zenodo.3483785
10.5281/zenodo.3483786	true	10.5281/zenodo.3483787
10.5281/zenodo.3483788	true	10.5281/zenodo.3483789
10.5281/zenodo.3483792	true	10.5281/zenodo.3483793
10.5281/zenodo.3520502	true	10.5281/zenodo.3864993
10.5281/zenodo.3571070	true
10.5281/zenodo.3571071	false
10.5281/zenodo.3605385	true	10.5281/zenodo.3605386
10.5281/zenodo.3606439	true	10.5281/zenodo.3613573
10.5281/zenodo.3606440	true	10.5281/zenodo.3613573
10.5281/zenodo.3725636	true	10.5281/zenodo.3725637
10.5281/zenodo.3725669	true	10.5281/zenodo.3725670
10.5281/zenodo.3832218	true
10.5281/zenodo.3832219	false
10.5281/zenodo.4492639	true	10.5281/zenodo.3997184
10.5281/zenodo.6582985	true	10.5281/zenodo.10183982
10.5281/zenodo.7035350	true	10.5281/zenodo.5767451

[comcon1]

It's not true. I just came to the last link.

b4f/866/b4f866c0dabffa6cd891e91841591d46590f34aa/a231c358dd8c0b7bb4cf558ccdbf022373354a9a/README.yaml:DOI: 10.5281/zenodo.3474863

[batukav]

you're right, it's not correct. the logic seems different than I thought. I'll double check this and update the list.

[comcon1]

From @batukav's last letter.

Missing Zenodo DOIs in BilayerData

Generated: 2026-02-14 10:12:09

• Total unique DOIs in BilayerData: 469
• Total unique DOIs in satellite repos: 309
• Candidate missing (before version check): 108
• Truly missing (no version in BilayerData): 46
• Matched via version check: 62

All candidate DOIs and version status

missing full doi	multiple versions on Zenodo	matching version DOI on BilayerData
10.5281/zenodo.12652	false
10.5281/zenodo.12654	false
10.5281/zenodo.12743	false
10.5281/zenodo.13279	true	10.5281/zenodo.4643875
10.5281/zenodo.13281	true	10.5281/zenodo.4643914
10.5281/zenodo.13282	true	10.5281/zenodo.4643899
10.5281/zenodo.13283	true	10.5281/zenodo.4643985
10.5281/zenodo.13286	true	10.5281/zenodo.4644028
10.5281/zenodo.13392	false
10.5281/zenodo.13393	false
10.5281/zenodo.13791	true	10.5281/zenodo.5734452
10.5281/zenodo.13821	false
10.5281/zenodo.13877	true	10.5281/zenodo.3252052
10.5281/zenodo.13946	true	10.5281/zenodo.4740115
10.5281/zenodo.15548	true	10.5281/zenodo.6656031
10.5281/zenodo.16830	false
10.5281/zenodo.17004	false
10.5281/zenodo.17208	false
10.5281/zenodo.30904	false
10.5281/zenodo.32496	true	10.5281/zenodo.4750862
10.5281/zenodo.34415	false
10.5281/zenodo.55318	false
10.5281/zenodo.55322	false
10.5281/zenodo.57845	true
10.5281/zenodo.60607	true	10.5281/zenodo.3243328
10.5281/zenodo.61992	true	10.5281/zenodo.3238157
10.5281/zenodo.153947	false
10.5281/zenodo.154346	true	10.5281/zenodo.3243329
10.5281/zenodo.159759	true	10.5281/zenodo.3237420
10.5281/zenodo.167336	false
10.5281/zenodo.209070	false
10.5281/zenodo.209080	false
10.5281/zenodo.209381	false
10.5281/zenodo.209391	false
10.5281/zenodo.887397	true	10.5281/zenodo.887398
10.5281/zenodo.887399	true	10.5281/zenodo.887400
10.5281/zenodo.1011095	true	10.5281/zenodo.1011096
10.5281/zenodo.1011104	false
10.5281/zenodo.1120287	false
10.5281/zenodo.1129430	true	10.5281/zenodo.1129431
10.5281/zenodo.1129434	true	10.5281/zenodo.1129435
10.5281/zenodo.1134869	true
10.5281/zenodo.1135142	false
10.5281/zenodo.1148495	false
10.5281/zenodo.1167532	false
10.5281/zenodo.1210255	true
10.5281/zenodo.1210256	true
10.5281/zenodo.1227256	true
10.5281/zenodo.1227257	true
10.5281/zenodo.1227272	true
10.5281/zenodo.1230169	true	10.5281/zenodo.1230170
10.5281/zenodo.1250969	false
10.5281/zenodo.1250975	false
10.5281/zenodo.1283334	true	10.5281/zenodo.1283335
10.5281/zenodo.1288296	true	10.5281/zenodo.1288297
10.5281/zenodo.1293761	true	10.5281/zenodo.1293762
10.5281/zenodo.1293812	true	10.5281/zenodo.1293813
10.5281/zenodo.1293852	true
10.5281/zenodo.1293853	false
10.5281/zenodo.1293854	true
10.5281/zenodo.1293855	false
10.5281/zenodo.1293888	true	10.5281/zenodo.1293889
10.5281/zenodo.1293904	true	10.5281/zenodo.1293905
10.5281/zenodo.1293927	true	10.5281/zenodo.1293928
10.5281/zenodo.1293931	true	10.5281/zenodo.1293932
10.5281/zenodo.1293940	true	10.5281/zenodo.1293941
10.5281/zenodo.1293956	true	10.5281/zenodo.1293957
10.5281/zenodo.1306799	true	10.5281/zenodo.1306800
10.5281/zenodo.1306820	true	10.5281/zenodo.1306821
10.5281/zenodo.1319601	true
10.5281/zenodo.1404040	true
10.5281/zenodo.1409551	true
10.5281/zenodo.1434990	false
10.5281/zenodo.1475284	true	10.5281/zenodo.1475285
10.5281/zenodo.1487760	true	10.5281/zenodo.1487761
10.5281/zenodo.2532248	true	10.5281/zenodo.2542176
10.5281/zenodo.2532249	true	10.5281/zenodo.2542176
10.5281/zenodo.2542134	true	10.5281/zenodo.2542135
10.5281/zenodo.2542150	true	10.5281/zenodo.2542151
10.5281/zenodo.2542163	true	10.5281/zenodo.2542164
10.5281/zenodo.2572897	true	10.5281/zenodo.3378992
10.5281/zenodo.2573530	true	10.5281/zenodo.2573531
10.5281/zenodo.2573905	true	10.5281/zenodo.4386514
10.5281/zenodo.2574490	true	10.5281/zenodo.2574491
10.5281/zenodo.2574533	true	10.5281/zenodo.2578069
10.5281/zenodo.2577305	true	10.5281/zenodo.4424934
10.5281/zenodo.2579675	false
10.5281/zenodo.2633773	true	10.5281/zenodo.3269320
10.5281/zenodo.2641986	true	10.5281/zenodo.2641987
10.5281/zenodo.3378970	true	10.5281/zenodo.4424292
10.5281/zenodo.3474862	true	10.5281/zenodo.3474863
10.5281/zenodo.3483784	true	10.5281/zenodo.3483785
10.5281/zenodo.3483786	true	10.5281/zenodo.3483787
10.5281/zenodo.3483788	true	10.5281/zenodo.3483789
10.5281/zenodo.3483792	true	10.5281/zenodo.3483793
10.5281/zenodo.3520502	true	10.5281/zenodo.3864993
10.5281/zenodo.3571070	true
10.5281/zenodo.3571071	false
10.5281/zenodo.3605385	true	10.5281/zenodo.3605386
10.5281/zenodo.3606439	true	10.5281/zenodo.3613573
10.5281/zenodo.3606440	true	10.5281/zenodo.3613573
10.5281/zenodo.3725636	true	10.5281/zenodo.3725637
10.5281/zenodo.3725669	true	10.5281/zenodo.3725670
10.5281/zenodo.3832218	true
10.5281/zenodo.3832219	false
10.5281/zenodo.4492639	true	10.5281/zenodo.3997184
10.5281/zenodo.6582985	true	10.5281/zenodo.10183982
10.5281/zenodo.7035350	true	10.5281/zenodo.5767451

[comcon1]

Looks fine. There are a lot of UA systems. Please deal with the problem of multiply identical mappings. Use the proper mapping file and put the name of the mappings for removal to the corresponding issue.

[comcon1]

I've done this one: 10.5281/zenodo.3832219 (the last one)

[batukav]

missing full doi | multiple versions on Zenodo | matching version DOI on BilayerData

• 10.5281/zenodo.12652 | false |  
• 10.5281/zenodo.12654 | false |  
• 10.5281/zenodo.12743 | false |  
• 10.5281/zenodo.13279 | true | 10.5281/zenodo.4643875
• 10.5281/zenodo.13281 | true | 10.5281/zenodo.4643914
• 10.5281/zenodo.13282 | true | 10.5281/zenodo.4643899
• 10.5281/zenodo.13283 | true | 10.5281/zenodo.4643985
• 10.5281/zenodo.13286 | true | 10.5281/zenodo.4644028
• 10.5281/zenodo.13392 | false |  
• 10.5281/zenodo.13393 | false |  
• 10.5281/zenodo.13791 | true | 10.5281/zenodo.5734452
• 10.5281/zenodo.13821 | false |  
• 10.5281/zenodo.13877 | true | 10.5281/zenodo.3252052
• 10.5281/zenodo.13946 | true | 10.5281/zenodo.4740115
• 10.5281/zenodo.15548 | true | 10.5281/zenodo.6656031
• 10.5281/zenodo.16830 | false |  
• 10.5281/zenodo.17004 | false |  
• 10.5281/zenodo.17208 | false |  
• 10.5281/zenodo.30904 | false |  
• 10.5281/zenodo.32496 | true | 10.5281/zenodo.4750862
• 10.5281/zenodo.34415 | false |  
• 10.5281/zenodo.55318 | false |  
• 10.5281/zenodo.55322 | false |  
• 10.5281/zenodo.57845 | true |  
• 10.5281/zenodo.60607 | true | 10.5281/zenodo.3243328
• 10.5281/zenodo.61992 | true | 10.5281/zenodo.3238157
• 10.5281/zenodo.153947 | false |  
• 10.5281/zenodo.154346 | true | 10.5281/zenodo.3243329
• 10.5281/zenodo.159759 | true | 10.5281/zenodo.3237420
• 10.5281/zenodo.167336 | false |  
• 10.5281/zenodo.209070 | false |  
• 10.5281/zenodo.209080 | false |  
• 10.5281/zenodo.209381 | false |  
• 10.5281/zenodo.209391 | false |  
• 10.5281/zenodo.887397 | true | 10.5281/zenodo.887398
• 10.5281/zenodo.887399 | true | 10.5281/zenodo.887400
• 10.5281/zenodo.1011095 | true | 10.5281/zenodo.1011096
• 10.5281/zenodo.1011104 | false |  
• 10.5281/zenodo.1120287 | false |  
• 10.5281/zenodo.1129430 | true | 10.5281/zenodo.1129431
• 10.5281/zenodo.1129434 | true | 10.5281/zenodo.1129435
• 10.5281/zenodo.1134869 | true |  
• 10.5281/zenodo.1135142 | false |  
• 10.5281/zenodo.1148495 | false |  
• 10.5281/zenodo.1167532 | false |  
• 10.5281/zenodo.1210255 | true |  
• 10.5281/zenodo.1210256 | true |  
• 10.5281/zenodo.1227256 | true |  
• 10.5281/zenodo.1227257 | true |  
• 10.5281/zenodo.1227272 | true |  
• 10.5281/zenodo.1230169 | true | 10.5281/zenodo.1230170
• 10.5281/zenodo.1250969 | false |  
• 10.5281/zenodo.1250975 | false |  
• 10.5281/zenodo.1283334 | true | 10.5281/zenodo.1283335
• 10.5281/zenodo.1288296 | true | 10.5281/zenodo.1288297
• 10.5281/zenodo.1293761 | true | 10.5281/zenodo.1293762
• 10.5281/zenodo.1293812 | true | 10.5281/zenodo.1293813
• 10.5281/zenodo.1293852 | true |  
• 10.5281/zenodo.1293853 | false |  
• 10.5281/zenodo.1293854 | true |  
• 10.5281/zenodo.1293855 | false |  
• 10.5281/zenodo.1293888 | true | 10.5281/zenodo.1293889
• 10.5281/zenodo.1293904 | true | 10.5281/zenodo.1293905
• 10.5281/zenodo.1293927 | true | 10.5281/zenodo.1293928
• 10.5281/zenodo.1293931 | true | 10.5281/zenodo.1293932
• 10.5281/zenodo.1293940 | true | 10.5281/zenodo.1293941
• 10.5281/zenodo.1293956 | true | 10.5281/zenodo.1293957
• 10.5281/zenodo.1306799 | true | 10.5281/zenodo.1306800
• 10.5281/zenodo.1306820 | true | 10.5281/zenodo.1306821
• 10.5281/zenodo.1319601 | true |  
• 10.5281/zenodo.1404040 | true |  
• 10.5281/zenodo.1409551 | true |  
• 10.5281/zenodo.1434990 | false |  
• 10.5281/zenodo.1475284 | true | 10.5281/zenodo.1475285
• 10.5281/zenodo.1487760 | true | 10.5281/zenodo.1487761
• 10.5281/zenodo.2532248 | true | 10.5281/zenodo.2542176
• 10.5281/zenodo.2532249 | true | 10.5281/zenodo.2542176
• 10.5281/zenodo.2542134 | true | 10.5281/zenodo.2542135
• 10.5281/zenodo.2542150 | true | 10.5281/zenodo.2542151
• 10.5281/zenodo.2542163 | true | 10.5281/zenodo.2542164
• 10.5281/zenodo.2572897 | true | 10.5281/zenodo.3378992
• 10.5281/zenodo.2573530 | true | 10.5281/zenodo.2573531
• 10.5281/zenodo.2573905 | true | 10.5281/zenodo.4386514
• 10.5281/zenodo.2574490 | true | 10.5281/zenodo.2574491
• 10.5281/zenodo.2574533 | true | 10.5281/zenodo.2578069
• 10.5281/zenodo.2577305 | true | 10.5281/zenodo.4424934
• 10.5281/zenodo.2579675 | false |  
• 10.5281/zenodo.2633773 | true | 10.5281/zenodo.3269320
• 10.5281/zenodo.2641986 | true | 10.5281/zenodo.2641987
• 10.5281/zenodo.3378970 | true | 10.5281/zenodo.4424292
• 10.5281/zenodo.3474862 | true | 10.5281/zenodo.3474863
• 10.5281/zenodo.3483784 | true | 10.5281/zenodo.3483785
• 10.5281/zenodo.3483786 | true | 10.5281/zenodo.3483787
• 10.5281/zenodo.3483788 | true | 10.5281/zenodo.3483789
• 10.5281/zenodo.3483792 | true | 10.5281/zenodo.3483793
• 10.5281/zenodo.3520502 | true | 10.5281/zenodo.3864993
• 10.5281/zenodo.3571070 | true |  
• 10.5281/zenodo.3571071 | false |  
• 10.5281/zenodo.3605385 | true | 10.5281/zenodo.3605386
• 10.5281/zenodo.3606439 | true | 10.5281/zenodo.3613573
• 10.5281/zenodo.3606440 | true | 10.5281/zenodo.3613573
• 10.5281/zenodo.3725636 | true | 10.5281/zenodo.3725637
• 10.5281/zenodo.3725669 | true | 10.5281/zenodo.3725670
• 10.5281/zenodo.3832218 | true |  
• 10.5281/zenodo.3832219 | false |  
• 10.5281/zenodo.4492639 | true | 10.5281/zenodo.3997184
• 10.5281/zenodo.6582985 | true | 10.5281/zenodo.10183982
• 10.5281/zenodo.7035350 | true | 10.5281/zenodo.5767451