1,739 research outputs found
phenoscape/phenoscape-kb-services: Release 2.0
No full textWhat's Changed
Enables Docker build for this application by @hlapp in https://github.com/phenoscape/phenoscape-kb-services/pull/52
Query by publications by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/54
Restore TSV output for taxon list output by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/60
Implement preliminary service providing Jaccard similarity score for a pair of character states by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/61
Add missing import. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/62
Correct services to ignore limit if <1. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/65
Update from swagger hub to fix study query doc. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/66
Service for pairwise similarity of list of ontology classes by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/67
Include entity in OntoTrace query including its parts. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/71
Generated code by SwaggerHub by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/72
Generated code by SwaggerHub by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/74
Created service for computing ancestor matrix by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/75
Issue 77 by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/78
Document subsumer matrix service. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/79
Make sort case-insensitive by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/80
Swaggerhub by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/84
Update matrix service to take JSON array of IRIs. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/85
Generated code by SwaggerHub by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/86
Generated code by SwaggerHub by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/88
Support POST for OntoTrace. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/87
Swaggerhub by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/96
Generated code by SwaggerHub by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/97
Generated code by SwaggerHub by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/99
Generated code by SwaggerHub by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/100
Make ic_disparity query parameter names consistent. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/101
Generated code by SwaggerHub by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/102
Return matrix for study as application/xml. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/103
Added method for executing SPARQL ASK queries. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/105
Generated code by SwaggerHub by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/107
Generated code by SwaggerHub by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/108
Implement services to handle queries for inferred presence/absence. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/110
New presence absence matrix branch by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/111
Generalize term search. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/115
Generated code by SwaggerHub by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/117
Generated code by SwaggerHub by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/118
Generated code by SwaggerHub by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/120
Accept JSON array for definedBy. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/119
Add ui button to get dependency matrix by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/114
Merge master by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/123
Fix query parameter name by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/124
Fix space in sample data. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/125
Update media type to text/csv. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/126
Boost match rank of terms with text exactly equal to search text. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/131
Return only one label for ancestor and descendant queries. Fixes #129. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/132
Add newline in results EOF by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/133
Provide option to make use of part_of for ancestor and descendant queries. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/134
Swaggerhub by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/135
Fixes typos in /similarity/matrix documentation by @hlapp in https://github.com/phenoscape/phenoscape-kb-services/pull/140
Use correct media type for ancestor matrix service by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/142
Add POST to /term/labels and /entity/dependency services by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/143
Implement service providing frequency information for an ontology term according to some identified corpus by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/151
Allow caching of POST requests. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/152
Preserve user specified order of iris in dependency matrix by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/150
Support streaming response for TaxonPhenotypeAnnotations TSV (and more) by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/153
Add documentation for taxon annotations query and annotation sources query. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/155
Document publication parameter. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/158
Return character id and label in the results of the study/phenotype kb-service by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/156
Accept JSON arrays for all IRI lists. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/159
Enable content negotiation with streaming annotations response. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/160
Migrate matrix renderer test to utest by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/164
Fix #26: Annotate ontotrace matrix with variable status by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/166
Order text search results consistently for different values of limit by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/168
Document acceptance of json array of IRIs for kb services by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/169
Make character IRI and label available where needed. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/178
Combine character id and label into a single json object by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/180
Issue 139 - merge term labels by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/170
Add 'phenotype' parameter to query endpoints. For issue #148. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/181
Implement phenotype info service. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/185
Refinements to phenotype info service. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/186
Document phenotype info service. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/187
Retrieve dependency matrix with a single query. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/204
Fixes #167: Adds missing author to ontotrace matrix by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/205
Add implementation for similarity/frequency for genes corpus by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/206
Return null if label doesn't exist by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/209
Only show states that are linked to taxon in /phenotype/info. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/208
Update sparql-interpolator. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/213
Return only one label for a term. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/211
Convert None responses for Option values into 404. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/212
Change MinimalTerm label to Option[String]. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/214
Fix null pointer exception in query result. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/215
Update sbt to 1.3.8 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/235
Update scalaz-core to 7.2.30 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/236
Update scowl to 1.3.4 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/234
Update phenoscape-kb-ingest to 1.6.2 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/233
Update groovy-all to 2.4.19 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/231
Update apache-jena-libs to 3.14.0 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/230
Update owlapi-distribution to 4.2.9 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/229
Update sbt-native-packager to 1.3.25 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/226
Update utest to 0.7.4 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/223
Update scala. Remove guava. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/237
Update sbt-native-packager to 1.7.0 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/238
Update groovy-all to 2.5.10 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/240
Update owlapi-distribution to 4.5.15 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/239
Update commons-io to 2.6 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/227
Update to JavaConverters, remove warnings. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/241
Update akka-stream-alpakka-xml to 1.1.2 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/222
Update owlet to 1.6.2 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/232
Update akka-actor, akka-slf4j, akka-stream to 2.5.30 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/224
Update spray-json to 1.3.5 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/228
Update akka-http-cors to 0.3.4 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/219
Update logback-classic to 1.1.11 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/220
Update results json in api docs by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/248
Update akka-actor, akka-slf4j, akka-stream to 2.6.4 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/246
Update akka-http-cors to 0.4.2 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/244
Update logback-classic to 1.2.3 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/245
Update akka-http, akka-http-caching, ... to 10.1.11 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/225
Update owlet to 1.7 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/247
Fix missing results in ancestors & descendants services by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/218
Return 0 count for frequency query when term is not matched in SPARQL query by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/216
Include character, state, and cell IRIs in matrix output. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/217
Fixes #188: Return term source ontology by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/249
Update sbt to 1.3.9 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/250
Remove println by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/251
Update groovy-all to 2.5.11 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/253
Update sbt to 1.3.10 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/255
Update owlet to 1.8.1 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/259
Update akka-http-cors to 0.4.3 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/256
Update owlapi-distribution to 4.5.16 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/257
Issue 179 kb metadata by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/252
Update sbt-native-packager to 1.7.1 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/264
Update akka-actor, akka-slf4j, akka-stream to 2.6.5 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/263
Add synonym detail to taxon info by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/266
Fix some deprecation warnings. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/265
Reformat with new scalafmt configs by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/271
Update to new sparql-utils. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/276
Change scalafmt align setting by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/283
Update akka-http, akka-http-caching, ... to 10.1.12 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/269
Update apache-jena-libs to 3.15.0 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/273
Update groovy-all to 2.5.12 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/275
Update Scala version for Travis by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/285
Update sbt-native-packager to 1.7.2 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/270
Test automatic SPARQL result derivation. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/279
Update akka-actor, akka-slf4j, akka-stream to 2.6.6 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/291
Update akka-stream-alpakka-xml to 2.0.1 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/292
Update scalafmt-core to 2.5.3 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/278
Update sbt-native-packager to 1.7.3 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/289
Update sbt to 1.3.12 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/288
Update commons-io to 2.7 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/284
Update scalafmt-core to 2.6.0 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/293
Update akka-http-cors to 1.0.0 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/277
Make tests actually run. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/295
Update scalafmt-core to 2.6.1 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/296
Change phenotypic profiles method to work with the new monarch schema by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/183
Updates for new Gene model by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/297
Update owlapi-distribution to 4.5.17 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/301
Update sbt to 1.3.13 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/299
Update sbt-native-packager to 1.7.4 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/302
Update apache-jena-libs to 3.16.0 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/306
Update scalafmt-core to 2.6.4 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/308
Update groovy-all to 2.5.13 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/309
Update akka-actor, akka-slf4j, akka-stream to 2.6.8 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/307
Update groovy-all to 3.0.5 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/311
Fixes #90 - add option to include subclasses, or not, for entity and … by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/290
Update sbt to 1.4.0 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/335
Update scalafmt-core to 2.7.5 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/341
Bug fix; rewrite query using sparql interpolator by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/344
Update sbt-native-packager to 1.7.6 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/340
Update owlapi-distribution to 4.5.18 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/345
Update sbt to 1.4.1 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/343
Update commons-io to 2.8.0 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/322
Update utest to 0.7.5 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/318
Update sbt to 1.4.4 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/356
Update utest to 0.7.7 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/375
Update scalaz-core to 7.2.31 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/373
Don't return owl:Thing in ancestor results. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/383
Update sbt to 1.4.7 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/381
Update sbt-native-packager to 1.8.0 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/369
Update akka-actor, akka-slf4j, akka-stream to 2.6.12 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/379
Update sparql-utils, sparql-utils-owlapi to 1.3 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/360
Update spray-json to 1.3.6 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/350
Roll back changes to taxon info return format. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/384
Create scala.yml by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/385
Update scala.yml by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/386
Services new data model by @Shalsh23 in https://github.com/phenoscape/phenoscape-kb-services/pull/329
Update scala-library to 2.12.13 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/394
Allow return of all search results using limit < 1. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/395
Update sparql-utils, sparql-utils-owlapi to 1.3.1 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/396
Update apache-jena-libs to 3.17.0 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/357
Update akka-http, akka-http-caching, ... to 10.1.14 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/392
Update akka-stream-alpakka-xml to 2.0.2 by @scala-steward in https://github.com/phenoscape/phenoscape-kb-services/pull/327
Support search and info for genes without phenotype annotations in switch to Monarch data. by @balhoff in https://github.com/phenoscape/phenoscape-kb-services/pull/399
Full Changelog: https://github.com/phenoscape/phenoscape-kb-services/compare/v0.5...v2.
PDBe-KB: collaboratively defining the biological context of structural data
No full textThe Protein Data Bank in Europe – Knowledge Base (PDBe-KB, https://pdbe-kb.org) is an open collaboration between world-leading specialist data resources contributing functional and biophysical annotations derived from or relevant to the Protein Data Bank (PDB). The goal of PDBe-KB is to place macromolecular structure data in their biological context by developing standardised data exchange formats and integrating functional annotations from the contributing partner resources into a knowledge graph that can provide valuable biological insights. Since we described PDBe-KB in 2019, there have been significant improvements in the variety of available annotation data sets and user functionality. Here, we provide an overview of the consortium, highlighting the addition of annotations such as predicted covalent binders, phosphorylation sites, effects of mutations on the protein structure and energetic local frustration. In addition, we describe a library of reusable web-based visualisation components and introduce new features such as a bulk download data service and a novel superposition service that generates clusters of superposed protein chains weekly for the whole PDB archive.ELIXIR [IDP implementation study]; Biotechnology and Biological Sciences Research Council via the 3D-Gateway [BB/T01959X/1]; FunPDBe [BB/P024351/1]; European Molecular Biology Laboratory-European Bioinformatics Institute who supported this work; J.D. acknowledges support from the Ministry of Education, Youth and Sport of the Czech Republic [INBIO CZ.02.1.01/0.0/0.0/16_026/0008451]; R.S., K.B. and J.D. also acknowledge support from the Ministry of Education, Youth and Sport of the Czech Republic [ELIXIR-CZ LM2018131]; L.M. acknowledges support from the European Union's Horizon 2020 Programme (H2020-INFRAIA-2018-1) [823839]; Research Foundation Flanders (FWO) [G032816N, G042518N, G028821N]; W.V. acknowledges support from the Research Foundation Flanders (FWO) [G032816N, G028821N]; A.R. acknowledges support from the Fondazione Cassa Di Risparmio di Firenze [24316]; European Commission [101017567]; M.H.C. acknowledges the AIRC project to MHC [IG 23539]; J.F.-R. acknowledges support from the Spanish Ministry of Science and Innovation [PID2019-110167RB-I00]; N.R. acknowledges support from the Norwegian Research Council (Norges Forskningsråd) [288008]; E.D.L. acknowledges support from the European Union's Horizon 2020 research and innovation programme [819318]; M.J.E.S. acknowledges support from the Wellcome Trust [104955/Z/14/Z, 218242/Z/19/Z]. Funding for open access charge: Biotechnology and Biological Sciences Research Council grant [BB/T01959X/1]; Wellcome Trust [104955/Z/14/Z and 218242/Z/19/Z].Peer ReviewedCurrent PDBe-KB Consortium Members with Affiliations. (BSC author: Gonzalo Parra)
Mihaly Varadi1, Stephen Anyango, David Armstrong, John Berrisford, Preeti Choudhary, Mandar Deshpande, Nurul Nadzirin, Sreenath S. Nair, Lukas Pravda, Ahsan Tanweer, Bissan Al-Lazikani, Claudia Andreini, Geoffrey J. Barton, David Bednar, Karel Berka, Tom Blundell, Kelly P Brock, Jose Maria Carazo, Jiri Damborsky, Alessia David, Sucharita Dey, Roland Dunbrack, Juan Fernandez Recio, Franca Fraternali, Toby Gibson, Manuela Helmer-Citterich, David Hoksza, Thomas Hopf, David Jakubec, Natarajan Kannan, Radoslav Krivak, Manjeet Kumar, Emmanuel D Levy, Nir London, Jose Ramon Macias, Madhusudhan M. Srivatsan, Debora S Marks, Lennart Martens, Stuart A McGowan, Jake E McGreig, Vivek Modi, R. Gonzalo Parra, Gerardo Pepe16, Damiano Piovesan, Jaime Prilusky, Valeria Putignano, Leandro G. Radusky, Pathmanaban Ramasamy, Atilio O. Rausch, Nathalie Reuter, Luis A. Rodriguez, Nathan J Rollins, Antonio Rosato, Paweł Rubach, Luis Serrano, Gulzar Singh,Petr Skoda, Carlos Oscar S. Sorzano, Jan Stourac, Joanna I Sulkowska, Radka Svobodova, Natalia Tichshenko, Silvio C.E. Tosatto, Wim Vranken, Mark N Wass, Dandan Xue, Daniel Zaidman, Janet Thornton, Michael Sternberg, Christine Orengo, Sameer VelankarPostprint (published version
Hyojun dai toa bunzu. 18 , Hawai shoto hen /
No full textMap of Hawaii published in Japan in 1943.; Also available in an electronic version via the internet at: http://nla.gov.au/nla.map-vn6451628. 880-04 Inset: Shinjuwan oyobi Honoruru fukin -- Hawai shoto fukin (Sandoicchi shoto). Scale 1:9,000,000.880-04 Inset: 1-MO!KB'IC!5#i%[i%Ni%ki%k!0o
No full textThis is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
The attached file is the published version of the article.NHM Repositor
Stosunki intensywności linii Kb/Ka
No full textGENERAL INFORMATIONTitle of Dataset: Stosunki intensywności linii Kb/KaAuthor/Principal Investigator InformationName: Łukasz SyrockiORCID:https://orcid.org/0000-0001-6595-1139Institution: Institute of Plasma Physics and Laser MicrofusionAddress: Hery 23, 01-497 Warsaw, PolandEmail: lukasz.syrocki@gmail.comEmail2: lukasz.syrocki@ifpilm.plDate of data collection: 2024-03-25Geographic location of data collection: Warsaw, PolandInformation about funding sources that supported the collection of the data: This work was supported by the National Science Centre, Poland under grant number 2021/05/X/ST2/01664SHARING/ACCESS INFORMATIONLicenses/restrictions placed on the data: CC BY - Creative Commons Attribution 4.0Links to publications that cite or use the data: https://www.mdpi.com/1422-0067/24/6/5570Recommended citation for this dataset: @data{LCF5UZ_2024,author = {Syrocki, Łukasz},publisher = {RepOD},title = "{Stosunki intensywności linii Kb/Ka}",year = {2024},version = {WERSJA ROBOCZA},doi = {10.18150/LCF5UZ},url = {https://doi.org/10.18150/LCF5UZ}}DATA & FILE OVERVIEWPolish: Stosunki intensywności linii Kb/Ka dla różnych konfiguracji początkowych pierwiastków Co, Cu, Fe, Ni wyznaczone metodą MCDF (pakiet GRASP).English: Intensity ratios of the Kb/Ka lines for various configurations of the initial elements Co, Cu, Fe, Ni determined by the MCDF method (GRASP package).METHODOLOGICAL INFORMATIONMethods for processing the data: The raw theoretical data were obtained from "A GENERAL-PURPOSE RELATIVISTIC ATOMIC STRUCTURE PROGRAM" (GRASP).DATA-SPECIFIC INFORMATION FOR EACH FILENumber of columns: 4Description of columns: Transition Energy (eV), Spont. trans. prob./sec., Oscillator strength </p
The Disappearance of an Author and the Emergence of a Genre: Niccolò da Poggibonsi and Pilgrimage Guidebooks between Manuscript and Print
No full textWhile the anonymous Viaggio da Venetia al Sancto Sepolchro et al Monte Sinai, first published in Venice in 1518, was the most popular Holy Land guidebook in Renaissance Italy, the historical origins of the book have never been fully understood. From four illustrated versions of an earlier manuscript guide, the Libro d’Oltramare (1346 –50), one can hypothesize about both the text and its author. The ultimate prototype for the Viaggio da Venetia was very likely one or more of these illustrated manuscripts, and the original author of both the text and illustrations was the Franciscan pilgrim Niccoloda Poggibonsi. Despite the eventual erosion of his name from the printed versions of the guidebook, the assertiveness and originality of the author parallels the production of other vernacular literature in mid-fourteenth-century Italy. Unlike Latin guidebooks of previous centuries, the intent to include illustrations that re-create the pilgrimage experience and the unprecedented descriptiveness of the prose together suggest that the book can be considered the foundational text for the genre of the illustrated pilgrimage guidebook.published_or_final_versio
Overactive NF-KB signaling as a druggable target and evaluation of parthenolide an NF-KB inhibitor in canine cancer
No full textIncludes bibliographical references.2022 Fall.This study provides a unique translational research opportunity to help both humans and dogs diagnosed with diseases that carry dismal prognoses in both species: histiocytic sarcoma (HS), hemangiosarcoma (HSA), and disseminated mastocytosis (MCT). Lymphoma is one of the most common cancer types affecting dogs and humans, and therefore, novel therapeutic approaches are always needed. For all of these cancer types, dogs and human cancers share common molecular abnormalities, consistent with a conserved pathogenesis between species. Relative to traditional murine models for human cancers, dogs are genetically diverse, large mammals with heterogeneous, spontaneous tumors. Dogs generally receive good medical care and share the environmental factors with humans, and accordingly, dogs with spontaneous tumors are an excellent model for human oncology generally. Additionally, although disseminated HS, MCT and visceral HSA are exceedingly rare diseases in humans, they are more common in some dog breeds, giving us the opportunity to study this disease in a larger population than would otherwise be available. Therapeutics evaluated in dogs with these diseases stand to benefit both canine and human patients. NF-kB proteins are a family of structurally related, eukaryotic transcription factors that have 400+ genetic targets, and are involved in many vital cellular processes, including innate immunity, inflammatory responses, development, cellular growth, and survival. Not surprisingly, overactivation of NF-kB is a feature of many chronic disease processes, including cardiac disease, neurodegenerative disease, immune-mediated disease, and cancer. While NF-kB overactivation has been documented extensively in human oncology, there is a relative paucity of data documenting the same phenomenon in veterinary medicine. As part of this study, large scale validation of NF-kB overactivation was performed in canine cancer via immunohistochemistry of 215 tumor samples (lymphoma, HS, HSA, and MCT). Antibodies were validated for use via western blot, immortalized cell pellets, and evaluation of normal canine tissues. In addition to validation of NF-kB overactivation, assays were performed to assess the therapeutic potential of parthenolide (PTL), a known, canonical NF-kB signaling inhibitor with additional mechanisms of antineoplastic activity, including alteration of cellular redox balance. Growth inhibition assays were performed with canine cell lines and primary lymphoma cells isolated from canine patients, using PTL alone or in combination with redox-perturbing standard-of-care therapeutics. Cell death was assessed using flow cytometry. Immunofluorescence was used to assess NF-kB localization, western blot was used to assess NF-kB activity with and without PTL, and canine cells were transfected with a reporter gene cassette containing the NFkB consensus sequence followed by firefly luciferase gene to study the effect of PTL on NF-kB-related luminescence. PTL's effects on glutathione and reactive oxygen species generation were assessed with a colorimetric assay and a fluorescent H2DCFDA assay, respectively. Genetic expression changes were assessed with RNA sequencing of HS cells, with and without PTL treatment. A mouse model of disseminated HS was created with NF-kB luminescent cells to study the effect of PTL on this disease in vivo. Many spontaneous canine tumor samples have nuclear p65 and p100/p52 IHC staining that is of greater magnitude than observed in comparable, normal cell populations, indicating the promise of PTL and other therapeutics that target aberrant NF-kB signaling. Canine cell lines and primary cells are sensitive to PTL and undergo dose-dependent apoptosis following exposure to drug. PTL exposure also leads to glutathione depletion, reactive oxygen species generation, and NF-kB inhibition in canine cells. Standard-of-care therapeutics broadly synergize with PTL. In two canine HS cell lines, genetic expression of NF-kB pathway signaling partners is downregulated with PTL therapy. Preliminary data suggest that PTL inhibits NF-kB activity of cells in a mouse model of disseminated HS. Overall, these data support further investigation of compounds that can antagonize canonical and alternative NF-kB pathway signaling, which are overactivated in canine lymphoma, HS, HSA, and MCT disease. PTL is one promising therapeutic that acts, in part, via canonical NF-kB antagonism in canine neoplasms. Further investigation of this compound in vivo is underway in a mouse model of disseminated HS, and if this study is successful, it will provide strong justification for clinical trials with this compound in dogs
Kirkwood-Buff integrals from molecular simulation
No full textThe Kirkwood-Buff (KB) theory provides a rigorous framework to predict thermodynamic properties of isotropic liquids from the microscopic structure. Several thermodynamic quantities relate to KB integrals, such as partial molar volumes. KB integrals are expressed as integrals of RDFs over volume but can also be obtained from density fluctuations in the grand-canonical ensemble. Various methods have been proposed to estimate KB integrals from molecular simulation. In this work, we review the available methods to compute KB integrals from molecular simulations of finite systems, and particular attention is paid to finite-size effects. We also review various applications of KB integrals computed from simulations. These applications demonstrate the importance of computing KB integrals for relating findings of molecular simulation to macroscopic thermodynamic properties of isotropic liquids.Accepted Author ManuscriptEngineering Thermodynamic
Author-Kit
No full text[SC 2020] output from commands that gather execution environment information.
# Environment information of Sunway Taihulight:
1. MPI version
bsub -I -n 1 -q q_sw_expr ./mpichversion
Job has been submitted to queue
waiting for dispatch ...
dispatching ...
MVAPICH2 Version: 2.2a
MVAPICH2 Release date: Mon Aug 17 20:00:00 EDT 2015
MVAPICH2 Device: ch3:mrail
MVAPICH2 configure: --without-cma --with-rdma=gen2 -prefix=/usr/sw-mpp/mpi2/mpiswgcc --with-pm=no --with-ib-include=/usr/sw-mpp/include --with-ib-libpath=/usr/sw-mpp/lib --enable-threads=single --enable-cxx --enable-f77 --enable-fc --enable-romio --with-ch3-rank-bits=32 --without-mpe --without-hwloc --disable-rdma-cm --disable-mcast --with-atomic-primitives=no --disable-fuse --disable-shared --enable-static --with-cross=crossfile --disable-registration-cache --host=sw --disable-smpcoll
MVAPICH2 CC: sw5gcc -mhost -DCONFIG_SWIB -DNDEBUG -DNVALGRIND -O2
MVAPICH2 CXX: sw5g++ -mhost -DNDEBUG -DNVALGRIND -O2
MVAPICH2 F77: sw5gfortran -mhost -L/usr/sw-mpp/lib -O2
MVAPICH2 FC: sw5gfortran -mhost -O2
Job 48191998 has been finished.
2. uname -a
bsub -I -n 1 -q q_sw_expr uname -a
Job has been submitted to queue
waiting for dispatch ...
dispatching ...
Linux vn000001 3.8.0-sw5 # SMP Wed Apr 25 10:49:45 CST 2018 sw_64 GNU/Linux
Job 48192008 has been finished.
3. cpuinfo
bsub -I -n 1 -q q_sw_expr lscpu || cat /proc/cpuinfo
Job has been submitted to queue
waiting for dispatch ...
dispatching ...
vn000000: exec_task: execvp(/usr/bin/lscpu) failed. errno= 2, reason: No such file or directory
[48192041 ## Sun Apr 19 11:28:11 2020] warning: node [0]: user's mpe task: tid= 0, pid= 11761, exit_code= 2
Job 48192041 has been finished. exit_code is 2
bsub -I -n 1 -q q_sw_expr cat /proc/cpuinfo
Job has been submitted to queue
waiting for dispatch ...
dispatching ...
cpu : SW_64
cpu model : SW5
cpu variation : 1
cpu revision : 0
cpu serial number :
system type : shenwei
system variation : 0
system revision : 0
system serial number :
cycle frequency [Hz] : 1450000000
timer frequency [Hz] : 0.24
page size [bytes] : 8192
phys. address bits : 44
max. addr. space # : 255
BogoMIPS : 0.81
kernel unaligned acc : 0 (pc=0,va=0)
user unaligned acc : 848883545 (pc=4ff041fca8,va=5000281914)
platform string : N/A
cpus detected : 4
cpus active : 4
cpu active mask : 0000000000001111
cpus core_start : 000000000000000f
mem cycle freq : 500
L1 Icache : 64K, 2-way, 64b line
L1 Dcache : 64K, 2-way, 64b line
L2 cache : n/a
L3 cache : n/a
Job 48192044 has been finished.
4. meninfo
bsub -I -n 1 -q q_sw_expr cat /proc/meminfo
Job has been submitted to queue
waiting for dispatch ...
dispatching ...
MemTotal: 2038472 kB
MemFree: 372600 kB
Buffers: 0 kB
Cached: 1371984 kB
SwapCached: 0 kB
Active: 718224 kB
Inactive: 715008 kB
Active(anon): 131576 kB
Inactive(anon): 8 kB
Active(file): 586648 kB
Inactive(file): 715000 kB
Unevictable: 70912 kB
Mlocked: 2904 kB
SwapTotal: 0 kB
SwapFree: 0 kB
Dirty: 0 kB
Writeback: 0 kB
AnonPages: 132136 kB
Mapped: 4224 kB
Shmem: 24 kB
Slab: 22040 kB
SReclaimable: 5144 kB
SUnreclaim: 16896 kB
KernelStack: 4368 kB
PageTables: 328 kB
NFS_Unstable: 0 kB
Bounce: 0 kB
WritebackTmp: 0 kB
CommitLimit: 1019232 kB
Committed_AS: 200360 kB
VmallocTotal: 8388608 kB
VmallocUsed: 12208 kB
VmallocChunk: 8376400 kB
AnonHugePages: 0 kB
HugePages_Total: 0
HugePages_Free: 0
HugePages_Rsvd: 0
HugePages_Surp: 0
Hugepagesize: 8192 kB
======================= cg0 =====================
UserPages_Mem_size: 8192 MB
UserPages_Conti_Total: 7680 MB
UserPages_Conti_Free: 7680 MB
UserPages_Conti_Used: 0 MB
UserPages_Cross_Size: 0 MB
======================= cg1 =====================
UserPages_Mem_size: 8192 MB
UserPages_Conti_Total: 7680 MB
UserPages_Conti_Free: 7680 MB
UserPages_Conti_Used: 0 MB
UserPages_Cross_Size: 0 MB
======================= cg2 =====================
UserPages_Mem_size: 8192 MB
UserPages_Conti_Total: 7680 MB
UserPages_Conti_Free: 7680 MB
UserPages_Conti_Used: 0 MB
UserPages_Cross_Size: 0 MB
======================= cg3 =====================
UserPages_Mem_size: 8192 MB
UserPages_Conti_Total: 7680 MB
UserPages_Conti_Free: 7680 MB
UserPages_Conti_Used: 0 MB
UserPages_Cross_Size: 0 MB
Job 48192086 has been finished.
## Environment information of TianHe 2
we run script provided by Author-Kit on login node of TianHe2
#! /bin/sh
# Linux data-gathering commands; adjust as necessary for your platform.
#
# Be sure to remove any information from the output that would violate
# SC's double-blind review policies.
env | sed "s/USER/USER/g"
set -x
lsb_release -a
uname -a
lscpu || cat /proc/cpuinfo
cat /proc/meminfo
inxi -F -c0
lsblk -a
lsscsi -s
module list
nvidia-smi
(lshw -short -quiet -sanitize || lspci) | cat
the output is in file collect_environment-tianhe2-output.txt of current repository
Cryo-EM structure of a helicase loading intermediate containing ORC-Cdc6-Cdt1-MCM2-7 bound to DNA
No full text26.03.14 KB. Ok to accepted version to spiral, 6 months embargo expired
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