cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.11942465
title: Data for the internship at the MPI

description: Data for the internship at the MPI

Repositories

Code



protein-structure-analysis -- A snakemake pipeline that allows for  comparison of protein complexes using the USalign algorithm,  invesitgation of ligands using PLIP, plotting of a ramachandran profile, enumerating steric clashes, analysis of surface accessibility and plotting of the beta-factor column.

snakemake-template -- Tempate for snakemake that I used throughout my internship. In this repo, aliases are set for the shell, and frequently used dependencies are installed.

NeuralPlexer -- A snakemake pipeline  that uses Neuralplexer to predict Protein ligand interactions.

snakemake-tutorial -- A repository that contains an example pipeline  for DNA read mapping between two sample types. Made for the Snakemake seminar.

distance-map -- A python script that analyses possible contacts between subunits of a protein complex and output contacts maps for each interface, and a subunit interaction graph.

LLPS-prediction -- A snakemake pipeline to annotate uniprot proteomes with scores from the PSPhunter and Seq2Phase tools.

LLPS-analysis -- A snakemake pipeline that analyses the performance of recently published LLPS prediction tools.

complex-prediction -- A snakemake pipeline to predict protein protein complexes using the Combfold algorithm.

yeast-computational-pi-screen -- Analysis of Humphreys et al 2021


Presentations and talks



Snakemake seminar -- My presentation to introduce snakemake to the AG Walther department . Repo hosted here.

Final presentation -- Presentation of my findings. Repo hosted here


 

Description of the dataset

.
├── data
│   ├── main
│   │   ├── cluster-channeling
│   │   │   ├── store.ttl
│   │   │   ├── UP000005640
│   │   │   └── UP000006548
│   │   └── contact-channeling
│   │       ├── 2024-06-02-combfold-glycolysis
│   │       ├── 2024-06-10-combfold-glycolysis
│   │       ├── 2024-06-13-alpha-fold-glycolysis
│   │       ├── enolase-neural-plexer
│   │       ├── fold_2024_06_21_14_11_enolase
│   │       └── tca-cycle-metabolon
│   └── side
│       ├── folding-actin
│       │   └── 2024-06-04
│       ├── folding-IMDPH1
│       │   └── 2024-06-01
│       └── hd-zip
├── LICENSE
├── pixi.lock
├── pixi.toml
├── README.md
├── resources
│   └── rcsb
│       ├── 5TD9.pdb
│       └── download
├── results
│   └── metabolon-prediction
│       └── tm-scores
│           ├── af2_enolase
│           └── af3_enolase
└── workflow
    ├── envs
    │   └── structure-comparison.yml
    ├── help.sh
    ├── help.txt
    ├── scripts
    │   └── convert-cif-to-pdb.py
    └── Snakefile
DOI: 10.6084/m9.figshare.27247437.v1
title: Supplementary Material for: Association Between Changes in Preoperative Serum Creatinine and Acute Kidney Injury After Cardiac Surgery: A Retrospective Cohort Study

description: Introduction: Limited information exists regarding the impact of preoperative serum creatinine changes on cardiac surgery-associated acute kidney injury (CSA-AKI). This study aimed to investigate the development of AKI in patients with a baseline estimated glomerular filtration rate (eGFR) of ≥60 mL/min/1.73 m2 who present with an elevation in preoperative serum creatinine. Methods: This retrospective cohort study assessed patients who underwent open-heart surgery. Preoperative serum creatinine change was calculated as the ratio of the maximum preoperative serum creatinine value to the baseline creatinine (MCR). Patients were categorized into three groups based on MCR: non-elevation (≤1.0), mild elevation (1.0 to 1.5), and pronounced elevation (≥1.5). Multivariable logistic regression was used to estimate the risk of AKI, severe AKI, and non-recovery from AKI. Results: There were significant increases in the odds of AKI (adjusted odds ratio [OR], 1.42; 95% confidence interval [CI], 1.29–1.57; per 0.1 increase in MCR), severe AKI (adjusted OR, 1.28; 95% CI, 1.15–1.41), and AKI non-recovery (adjusted OR, 1.29; 95% CI, 1.16–1.43). Pronounced elevation in preoperative serum creatinine was associated with a higher risk of AKI (adjusted OR, 15.45; 95% CI, 6.63–36.00), severe AKI (adjusted OR, 3.62; 95% CI, 1.20–10.87), and AKI non-recovery (adjusted OR, 4.74; 95% CI, 1.63–13.89) than non–elevation. Mild elevation in preoperative serum creatinine was also significantly associated with AKI (adjusted OR, 3.76; 95% CI, 1.92–7.37). Conclusions: Elevation in preoperative serum creatinine from baseline was associated with an increased risk of AKI; even mild elevation significantly increased the risk of AKI.
DOI: 10.15468/dl.r7fy8c
title: Occurrence Download

description: A dataset containing 51720081 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "Country is India"
 ]
}

 The dataset includes 51720081 records from 3504 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019572-241007104925546/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dakmhr
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Beilschmiedia obconica C.K.Allen"
 ]
}

 The dataset includes 12 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0086303-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.q4krkq
title: Occurrence Download

description: A dataset containing 52 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lytorhynchus ridgewayi Boulenger, 1887"
 ]
}

 The dataset includes 52 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0292077-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h5zaht
title: Occurrence Download

description: A dataset containing 79 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Tanacetum punctatum (Desr.) Grierson"
 ]
}

 The dataset includes 79 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004576-230810091245214/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.strnc9
title: Occurrence Download

description: A dataset containing 109 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Occurrence evidence",
 "Country is Brazil",
 "TaxonKey is Ipomoea hederifolia L."
 ]
}

 The dataset includes 109 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0292108-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2bgxzf
title: Occurrence Download

description: A dataset containing 686 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "PublishingCountry is Colombia",
 {
 "and" : [
 "Country is Colombia",
 {
 "not" : {
 "Issue" : [
 "is Country coordinate mismatch"
 ]
 }
 }
 ]
 }
 ]
 },
 {
 "and" : [
 "TaxonKey is one of (Fungi)",
 "GadmGid is one of (COL.17_1)"
 ]
 }
 ]
}

 The dataset includes 686 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026816-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tpbug7
title: Occurrence Download

description: A dataset containing 891 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Brazil",
 "TaxonKey is Cuscuta racemosa C.Mart."
 ]
}

 The dataset includes 891 records from 82 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0292114-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tpzv9b
title: Occurrence Download

description: A dataset containing 15 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Spigelia amazonica Fern.Casas"
 ]
}

 The dataset includes 15 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0139403-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pbnr7t
title: Occurrence Download

description: A dataset containing 745 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is TRUE",
 "EventDate is less than or equal to 2022-08-04",
 "EventDate is greater than or equal to 2022-07-28",
 "DecimalLatitude is greater than or equal to 35",
 "DecimalLatitude is less than or equal to 72",
 "DecimalLongitude is greater than or equal to -86",
 "DecimalLongitude is less than or equal to -47"
 ]
}

 The dataset includes 745 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0415269-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7w6g7g
title: Occurrence Download

description: A dataset containing 3401 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Tanacetum balsamita L."
 ]
}

 The dataset includes 3401 records from 208 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004590-230810091245214/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fxuthb
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Arthroleptis troglodytes Poynton, 1963"
 ]
}

 The dataset includes 12 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0303783-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fmqhvj
title: Occurrence Download

description: A dataset containing 107665 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Populus alba L."
 ]
}

 The dataset includes 107665 records from 585 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0119183-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6ztk9q
title: Occurrence Download

description: A dataset containing 249 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Tanacetum argenteum (Lam.) Willd."
 ]
}

 The dataset includes 249 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004575-230810091245214/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h2bszg
title: Occurrence Download

description: A dataset containing 358 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Atelognathus nitoi (Barrio, 1973)"
 ]
}

 The dataset includes 358 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0303785-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uj4eg9
title: Occurrence Download

description: A dataset containing 8454 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Sander vitreus (Mitchill, 1818)"
 ]
}

 The dataset includes 8454 records from 60 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0042654-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.x2wjnd
title: Occurrence Download

description: A dataset containing 26 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Urochloa clavipila (Chiov.) Sosef"
 ]
}

 The dataset includes 26 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0098763-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z7b3c6
title: Occurrence Download

description: A dataset containing 2028 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lepus saxatilis F.Cuvier, 1823"
 ]
}

 The dataset includes 2028 records from 46 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0428626-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rmttnx
title: Occurrence Download

description: A dataset containing 5219 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cedrus atlantica (Endl.) Manetti ex Carriere",
 "HasCoordinate is true"
 ]
}

 The dataset includes 5219 records from 157 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0119194-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dcnyzx
title: Occurrence Download

description: A dataset containing 16299 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Centaurium littorale (Turner) Gilmour",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "Year is greater than or equal to 1990",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
}

 The dataset includes 16299 records from 96 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0163138-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z95ber
title: Occurrence Download

description: A dataset containing 1276 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Urochloa comata (Hochst. ex A.Rich.) Sosef"
 ]
}

 The dataset includes 1276 records from 59 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0098765-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tbpc2e
title: Occurrence Download

description: A dataset containing 150 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is COL.2.69_2",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Apis mellifera Linnaeus, 1758",
 "Year 2012-2022"
 ]
}

 The dataset includes 150 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022695-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mgzv83
title: Occurrence Download

description: A dataset containing 283 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Tanacetum audibertii (Req.) DC."
 ]
}

 The dataset includes 283 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004587-230810091245214/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8vfwwg
title: Occurrence Download

description: A dataset containing 105583 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Poaceae)",
 "HasCoordinate is true",
 "Country is South Africa"
 ]
}

 The dataset includes 105583 records from 78 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0151708-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.djdxpw
title: Occurrence Download

description: A dataset listing the 2 species recorded in GBIF matching the query:
{
 "and" : [
 "Country is Brazil",
 "TaxonKey is Phrynops geoffroanus (Schweigger, 1812)"
 ]
}

 The dataset's 2 records were derived from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028823-230810091245214/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mwatm8
title: Occurrence Download

description: A dataset containing 76 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "TaxonKey is Cleisostoma fuerstenbergianum Kraenzl."
 ]
}

 The dataset includes 76 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032399-230810091245214/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mvfj7p
title: Occurrence Download

description: A dataset containing 4180 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Suaeda australis (R.Br.) Moq."
 ]
}

 The dataset includes 4180 records from 77 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0236992-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.absz3s
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bulbophyllum polyphyllum Schltr."
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071121-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nxjpn7
title: Occurrence Download

description: A dataset containing 24 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-123.046874 35.460669,-123.046874 10.487811,-75.9375 10.487811,-75.9375 35.460669,-123.046874 35.460669))",
 {
 "or" : [
 "HasGeospatialIssue is false",
 "HasGeospatialIssue is true"
 ]
 },
 "DatasetKey is NHMO Bird collection"
 ]
}

 The dataset includes 24 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026157-151016162008034/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.48hhfn
title: Occurrence Download

description: A dataset containing 128 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Dobsonia crenulata K.Andersen, 1909"
 ]
}

 The dataset includes 128 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071143-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8x264b
title: Occurrence Download

description: A dataset containing 1798 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Oncidium sphacelatum Lindl., Catasetum integerrimum Hook.)"
 ]
}

 The dataset includes 1798 records from 105 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015169-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cg7f2t
title: Occurrence Download

description: A dataset containing 2693 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Cornus controversa Hemsl.)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 2693 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011267-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hthiqp
title: Occurrence Download

description: A dataset containing 10309 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Amaranthus albus Rodsch."
 ]
}

 The dataset includes 10309 records from 204 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026158-151016162008034/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.65c6z3
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bulbophyllum proboscideum (Gagnep.) Seidenf. & Smitinand"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071233-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4slsc7
title: Occurrence Download

description: A dataset containing 174 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bomarea pauciflora (Kunth) Herb.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 174 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026162-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.evvgs4
title: Occurrence Download

description: A dataset containing 19404 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Anura, Caudata)",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 19404 records from 57 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020433-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ccgq8r
title: Occurrence Download

description: A dataset containing 246018 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is France",
 "OccurrenceStatus is Present",
 "TaxonKey is Achillea millefolium L."
 ]
}

 The dataset includes 246018 records from 1901 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011277-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.