diff --git a/citations.html b/citations.html index f9aa9ebca..190185810 100644 --- a/citations.html +++ b/citations.html @@ -141,6 +141,7 @@

2023

  1. В,С.М. et al. (2023) ВЫЧИСЛИТЕЛЬНЫЙ АНАЛИЗ СТРУКТУРНОГО CОСТАВА ГЕНОМОВ КОРОНАВИРУСОВ. Доклады Белорусского государственного университета информатики и радиоэлектроники, 21, 104–113.
  2. Agboli,E. et al. (2023) Interaction of Mesonivirus and Negevirus with arboviruses and the RNAi response in Culex tarsalis-derived cells. Parasites & Vectors, 16, 361.
  3. Ahmad,N. et al. (2023) Biosynthetic Potential of Hypogymnia Holobionts: Insights into Secondary Metabolite Pathways. Journal of Fungi, 9, 546.
    4. +
  4. Ahmed,N.A. et al. (2023) Safety assessment of Enterococcus lactis strains complemented with comparative genomics analysis reveals probiotic and safety characteristics of the entire species. BMC Genomics, 24, 667.
  5. Multimodal epigenetic changes and altered NEUROD1 chromatin binding in the mouse hippocampus underlie FOXG1 syndrome (2023) Proceedings of the National Academy of Sciences, 120, e2122467120.
  6. Alvandi,H. et al. (2023) Pathovar-Specific PCR Method for Detection and Identification of Xanthomonas translucens pv. undulosa. Plant Disease.
  7. Anbazhagan,S. et al. (2023) Comparative genomics of Brucella abortus and Brucella melitensis unravels the gene sharing, virulence factors and SNP diversity among the standard, vaccine and field strains. International Microbiology.
    8. @@ -159,12 +160,14 @@

    2023

  8. Beerling,D. et al. (2023) Enhanced weathering in the U.S. Corn Belt delivers carbon removal with agronomic benefits.
  9. Belair,M. et al. (2023) Botryosphaeriaceae gene machinery: Correlation between diversity and virulence. Fungal Biology, 127, 1010–1031.
  10. Bennett-Keki,S. et al. (2023) Sex-biased gene expression in nutrient-sensing pathways. Proceedings of the Royal Society B: Biological Sciences, 290, 20222086.
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  11. Bennett-Keki,S. et al. (2023) Sex-biased gene expression in nutrient-sensing pathways. Proceedings of the Royal Society B: Biological Sciences, 290, 20222086.
  12. Bordel,S. et al. (2023) Genome sequence analysis and characterization of Bacillus altitudinis B12, a polylactic acid- and keratin-degrading bacterium. Molecular Genetics and Genomics, 298, 389–398.
  13. Bordel,S. et al. (2023) Genome sequence analysis and characterization of Bacillus altitudinis B12, a polylactic acid- and keratin-degrading bacterium. Molecular Genetics and Genomics, 298, 389–398.
  14. Boutigny,A.-L. et al. (2023) Direct Xylella fastidiosa whole genome sequencing from various plant species using targeted enrichment. Journal of Microbiological Methods, 208, 106719.
  15. Breidenbach,J.D. (2023) Harmful Algal Bloom Toxin Aerosol Exposure and Airway Inflammation.
  16. Broche,J. et al. (2023) Genome-wide deposition of 6-methyladenine in human DNA reduces the viability of HEK293 cells and directly influences gene expression. Communications Biology, 6, 1–12.
  17. Brück,P. et al. (2023) Ploidy in Vibrio natriegens: Very Dynamic and Rapidly Changing Copy Numbers of Both Chromosomes. Genes, 14, 1437.
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  18. Buchacher,T. et al. (2023) PIM kinases regulate early human Th17 cell differentiation. Cell Reports, 42, 113469.
  19. Camargo,C.H. et al. (2023) Genomic analysis and antimicrobial activity of β-lactam/β-lactamase inhibitors and other agents against KPC-producing Klebsiella pneumoniae clinical isolates from Brazilian hospitals. Scientific Reports, 13, 14603.
  20. Camargo,C.H. et al. (2023) Genomics and Antimicrobial Susceptibility of Clinical Pseudomonas aeruginosa Isolates from Hospitals in Brazil. Pathogens, 12, 918.
  21. Capitani,V. et al. (2023) Genome-Based Retrospective Analysis of a Providencia stuartii Outbreak in Rome, Italy: Broad Spectrum IncC Plasmids Spread the NDM Carbapenemase within the Hospital. Antibiotics, 12, 943.
    22. @@ -179,7 +182,7 @@

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  22. Carmo Santos,M.L. do et al. (2023) Proteomics analysis reveals three potential cacao target that interacts with Moniliophthora perniciosa NEP during witches broom disease. Physiological and Molecular Plant Pathology, 124, 101946.
  23. Dziuba,M.V. et al. (2023) Silent gene clusters encode magnetic organelle biosynthesis in a non-magnetotactic phototrophic bacterium. The ISME Journal, 17, 326–339.
  24. Emser,S.V. et al. (2023) Mitochondrial polymorphism m.3017C\textgreaterT of SHLP6 relates to heterothermy. Frontiers in Physiology, 14.
    25. -
  25. Esha,N.J.I. et al. (2023) Exploring the potential of fluoro-flavonoid derivatives as anti-lung cancer agents: DFT, molecular docking, and molecular dynamics techniques. International Journal of Quantum Chemistry, n/a, e27274.
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  26. Esha,N.J.I. et al. (2023) Exploring the potential of fluoro-flavonoid derivatives as anti-lung cancer agents: DFT, molecular docking, and molecular dynamics techniques. International Journal of Quantum Chemistry, n/a, e27274.
  27. Farias,K.S. et al. (2023) BASIDIN as a New Protein Effector of the Phytopathogen Causing Witche’s Broom Disease in Cocoa. International Journal of Molecular Sciences, 24, 11714.
  28. Farmiloe,G. et al. (2023) Structural Evolution of Gene Promoters Driven by Primate-Specific KRAB Zinc Finger Proteins. Genome Biology and Evolution, 15, evad184.
  29. Fatima,A. and Khan,M.A. (2023) Book of Abstracts of the 1st Colloquium for Bioinformatics Learning, Education, and Training. F1000Research, 12, 70.
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  30. Härdtner,C. et al. (2023) A comparative gene expression matrix in Apoe-deficient mice identifies unique and atherosclerotic disease stage-specific gene regulation patterns in monocytes and macrophages. Atherosclerosis, 371, 1–13.
  31. Hedhly,A. et al. (2023) S-Locus Genotyping in Japanese Plum by High Throughput Sequencing Using a Synthetic S-Loci Reference Sequence. International Journal of Molecular Sciences, 24, 3932.
  32. Heß,D. et al. (2023) Insight into the nodal cells transcriptome of the streptophyte green alga Chara braunii S276. Physiologia Plantarum, 175, e14025.
    33. +
  33. Hodzhev,Y. (2023) Analysis of blood microbiome dysbiosis in pulmonary sarcoidosis by decision tree model. Biotechnology & Biotechnological Equipment, 37, 2283133.
  34. Hosseinzadeh,S. and Hasanpur,K. (2023) Gene expression networks and functionally enriched pathways involved in the response of domestic chicken to acute heat stress. Frontiers in Genetics, 14.
  35. Howard,M. et al. (2023) Complete genome sequence of a human bacteremia isolate of Kalamiella piersonii. Microbiology Resource Announcements, 0, e00293–23.
  36. Huang,Y.-H. et al. (2023) A translational regulator MHZ9 modulates ethylene signaling in rice. Nature Communications, 14, 4674.
    37. @@ -205,6 +209,7 @@

    2023

  37. Izquierdo-Lara,R.W. et al. (2023) Rise and fall of SARS-CoV-2 variants in Rotterdam: Comparison of wastewater and clinical surveillance. Science of The Total Environment, 873, 162209.
  38. izzo,annalisa et al. (2023) Nucleophosmin 1 cooperates with the methyltransferase DOT1L to regulate H3K79me2 levels and DNA satellites expression at peri-nucleolar heterochromatin In Review.
  39. Jaki,L. et al. (2023) Total escape of SARS-CoV-2 from dual monoclonal antibody therapy in an immunocompromised patient. Nature Communications, 14, 1999.
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  40. Javed,M. et al. (2023) Unraveling the transcriptional network regulated by miRNAs in blast-resistant and blast-susceptible rice genotypes during Magnaporthe oryzae interaction. Gene, 886, 147718.
  41. Jeon,G.-T. et al. (2023) Tailored Multiplex Real-Time RT-PCR with Species-Specific Internal Positive Controls for Detecting SARS-CoV-2 in Canine and Feline Clinical Samples. Animals, 13, 602.
  42. Jesudoss Chelladurai,J.R.J. et al. (2023) Comparative Genomic Analysis and Species Delimitation: A Case for Two Species in the Zoonotic Cestode Dipylidium caninum. Pathogens, 12, 675.
  43. Jhinjharia,D. et al. (2023) A high-throughput structural dynamics approach for identification of potential agonists of FFAR4 for type 2 diabetes mellitus therapy. Journal of Biomolecular Structure and Dynamics, 0, 1–21.
    44. @@ -221,6 +226,7 @@

    2023

  44. Le Corre,L. and Padovani,D. (2023) Mechanism-based and computational modeling of hydrogen sulfide biogenesis inhibition: interfacial inhibition. Scientific Reports, 13, 7287.
  45. Lenz,M. et al. (2023) The Amyloid Precursor Protein Regulates Synaptic Transmission at Medial Perforant Path Synapses. Journal of Neuroscience, 43, 5290–5304.
  46. Lenz,M. et al. (2023) Denervated mouse CA1 pyramidal neurons express homeostatic synaptic plasticity following entorhinal cortex lesion. Frontiers in Molecular Neuroscience, 16.
    47. +
  47. Li,Y. et al. (2023) Proteogenomic data and resources for pan-cancer analysis. Cancer Cell, 41, 1397–1406.
  48. Liu,L. et al. (2023) A comprehensive review of bioinformatics tools for chromatin loop calling. Briefings in Bioinformatics, bbad072.
  49. Livingstone,M. et al. (2023) De Novo Whole-Genome Sequencing of Two Pathogenic Pasteurella multocida Type D:6 Strains Isolated from Pigs. Microbiology Resource Announcements, 12, e00098–23.
  50. Maki,J.J. et al. (2023) Species Delineation and Comparative Genomics within the Campylobacter ureolyticus Complex. Journal of Clinical Microbiology, 61, e00046–23.
    51. @@ -239,7 +245,9 @@

    2023

  51. Oger,F. et al. (2023) β-Cell–Specific E2f1 Deficiency Impairs Glucose Homeostasis, β-Cell Identity, and Insulin Secretion. Diabetes, 72, 1112–1126.
  52. Ohta,T. and Shiwa,Y. (2023) Hybrid Genome Assembly of Short and Long Reads in Galaxy. In, Arakawa,K. (ed), Nanopore Sequencing: Methods and Protocols, Methods in Molecular Biology. Springer US, New York, NY, pp. 15–30.
  53. Olagoke,O.C. et al. (2023) RPS6 transcriptional modulation in neural tissues of Nauphoeta cinerea during streptozotocin-associated sugar metabolism impairment. Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology, 263, 110785.
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  54. Oliveira,M.I.B.de et al. (2023) Cocoa apoplastome contains defense proteins against pathogens. https://doi.org/10.1094/PHYTO-03-23-0101-R.
  55. Palecanda,S. et al. (2023) Increasing complexity of opsin expression across stomatopod development. Ecology and Evolution, 13, e10121.
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  56. Palecanda,S. et al. (2023) Molecular Evolution of Malacostracan Short Wavelength Sensitive Opsins. Journal of Molecular Evolution.
  57. Pannhorst,K. et al. (2023) The non-classical major histocompatibility complex II protein SLA-DM is crucial for African swine fever virus replication. Scientific Reports, 13, 10342.
  58. Patel,U. et al. (2023) Bioprospecting phytochemicals of Rosmarinus officinalis L. for targeting SARS-CoV-2 main protease (Mpro): a computational study. Journal of Molecular Modeling, 29, 161.
  59. Pelos,G. et al. (2023) Fast proliferating and slowly migrating non-small cell lung cancer cells are vulnerable to decitabine and retinoic acid combinatorial treatment. International Journal of Cancer.
    60. @@ -255,6 +263,7 @@

    2023

  60. SAKAMOTO,H. et al. (2023) Detection of domestic cat hepadnavirus by next-generation sequencing and epidemiological survey in Japan. The Journal of Veterinary Medical Science, 85, 642–646.
  61. Sánchez-León,I. et al. (2023) Heteroresistance to Colistin in Clinical Isolates of Klebsiella pneumoniae Producing OXA-48. Antibiotics, 12, 1111.
  62. Schiml,V.C. et al. (2023) Integrative meta-omics in Galaxy and beyond. Environmental Microbiome, 18, 56.
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  63. Schoof,M. et al. (2023) Mouse models of pediatric high-grade gliomas with MYCN amplification reveal intratumoral heterogeneity and lineage signatures. Nature Communications, 14, 7717.
  64. Schüle,K.M. et al. (2023) Eomes restricts Brachyury functions at the onset of mouse gastrulation. Developmental Cell, 0.
  65. Schwabenland,M. et al. (2023) Neonatal immune challenge poses a sex-specific risk for epigenetic microglial reprogramming and behavioral impairment. Nature Communications, 14, 2721.
  66. Seckin Dinler,B. et al. (2023) The regulation of glutathione s-transferases by gibberellic acid application in salt treated maize leaves. Physiology and Molecular Biology of Plants, 29, 69–85.
    67. @@ -265,6 +274,7 @@

    2023

  67. Sheikh,T.M.M. et al. (2023) Volatile Organic Compounds Emitted by the Biocontrol Agent Pythium oligandrum Contribute to Ginger Plant Growth and Disease Resistance. Microbiology Spectrum, 0, e01510–23.
  68. Shi,S. et al. (2023) Modeling bile duct ischemia and reoxygenation injury in human cholangiocyte organoids for screening of novel cholangio-protective agents. eBioMedicine, 88, 104431.
  69. Siatra,P. et al. (2023) Return of the Tbx5; lineage-tracing reveals ventricular cardiomyocyte-like precursors in the injured adult mammalian heart. npj Regenerative Medicine, 8, 1–15.
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  70. Somashekhar,R. et al. (2023) Proceedings of the Joint 3rd International Conference on Bioinformatics and Data Science (ICBDS 2022) Springer Nature.
  71. Soorni,A. et al. (2023) Genome-wide screening and characterization of long noncoding RNAs involved in flowering/bolting of Lactuca sativa. BMC Plant Biology, 23, 3.
  72. Sozzoni,M. et al. (2023) A Chromosome-Level Reference Genome for the Black-Legged Kittiwake (Rissa tridactyla), a Declining Circumpolar Seabird. Genome Biology and Evolution, 15, evad153.
  73. Spanò,R. et al. (2023) Comparative Analysis of Bioactive Compounds in Two Globe Artichoke Ecotypes Sanitized and Non-Sanitized from Viral Infections. Plants, 12, 1600.
    74. diff --git a/events-ical.html b/events-ical.html index 6d8156191..3c70602cc 100644 --- a/events-ical.html +++ b/events-ical.html @@ -4,6 +4,48 @@ BEGIN:VCALENDAR +PRODID:-//jekyll//NONSGML v1.0//EN +VERSION:2.0 +CALSCALE:GREGORIAN +METHOD:PUBLISH +X-WR-CALNAME:UseGalaxy.eu Tool Updates for 2023-12-07 +X-WR-TIMEZONE:Europe/Berlin +BEGIN:VEVENT +ORGANIZER;CN=:MAILTO:?subject=UseGalaxy.eu%20Tool%20Updates%20for%202023-12-07 +DTSTART;VALUE=DATE: +DTEND;VALUE=DATE: +DTSTAMP;VALUE=DATE:T000000Z +CREATED;VALUE=DATE:20231207T000000Z +UID:@usegalaxy.eu +DESCRIPTION: +LOCATION: +SEQUENCE:0 +STATUS:CONFIRMED +SUMMARY:UseGalaxy.eu Tool Updates for 2023-12-07 +TRANSP:OPAQUE +END:VEVENT + +PRODID:-//jekyll//NONSGML v1.0//EN +VERSION:2.0 +CALSCALE:GREGORIAN +METHOD:PUBLISH +X-WR-CALNAME:UseGalaxy.eu Tool Updates for 2023-12-03 +X-WR-TIMEZONE:Europe/Berlin +BEGIN:VEVENT +ORGANIZER;CN=:MAILTO:?subject=UseGalaxy.eu%20Tool%20Updates%20for%202023-12-03 +DTSTART;VALUE=DATE: +DTEND;VALUE=DATE: +DTSTAMP;VALUE=DATE:T000000Z +CREATED;VALUE=DATE:20231203T000000Z +UID:@usegalaxy.eu +DESCRIPTION: +LOCATION: +SEQUENCE:0 +STATUS:CONFIRMED +SUMMARY:UseGalaxy.eu Tool Updates for 2023-12-03 +TRANSP:OPAQUE +END:VEVENT + PRODID:-//jekyll//NONSGML v1.0//EN VERSION:2.0 CALSCALE:GREGORIAN diff --git a/feed.xml b/feed.xml index af15f965d..e3be5619e 100644 --- a/feed.xml +++ b/feed.xml @@ -1,4 +1,186 @@ -Jekyll2023-12-03T02:52:22+01:00https://galaxyproject.eu/feed.xmlGalaxy EuropeThe European Galaxy InstanceUseGalaxy.eu Tool Updates for 2023-11-262023-11-26T00:00:00+01:002023-11-26T00:00:00+01:00https://galaxyproject.eu/posts/2023/11/26/tool-update<p>On 2023-11-26, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in <a href="https://build.galaxyproject.eu/job/usegalaxy-eu/job/install-tools/#419/">Jenkins Build #419</a></p> +Jekyll2023-12-08T18:15:32+01:00https://galaxyproject.eu/feed.xmlGalaxy EuropeThe European Galaxy InstanceUseGalaxy.eu Tool Updates for 2023-12-072023-12-07T00:00:00+01:002023-12-07T00:00:00+01:00https://galaxyproject.eu/posts/2023/12/07/tool-update<p>On 2023-12-07, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in <a href="https://build.galaxyproject.eu/job/usegalaxy-eu/job/install-tools/#421/">Jenkins Build #421</a></p> + +<h2 id="data-and-metadata-management">Data and Metadata Management</h2> + +<ul> + <li>eml2eal was updated to <a href="https://toolshed.g2.bx.psu.edu/view/ecology/eml2eal/248b03f124dd">248b03f124dd</a></li> + <li>eml2eal was updated to <a href="https://toolshed.g2.bx.psu.edu/view/ecology/eml2eal/409d9329d2be">409d9329d2be</a></li> + <li>makeeml was updated to <a href="https://toolshed.g2.bx.psu.edu/view/ecology/makeeml/642e31c435c9">642e31c435c9</a></li> +</ul> + +<h2 id="metabolomics">Metabolomics</h2> + +<ul> + <li>matchms_add_key was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/matchms_add_key/68fde0dc3d83">68fde0dc3d83</a></li> + <li>matchms_convert was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/matchms_convert/4845979fbe02">4845979fbe02</a></li> + <li>matchms_filtering was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/matchms_filtering/a4661ff81aa4">a4661ff81aa4</a></li> + <li>matchms_fingerprint_similarity was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/matchms_fingerprint_similarity/cbfd7c35e0a4">cbfd7c35e0a4</a></li> + <li>matchms_formatter was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/matchms_formatter/d888a64f7c2a">d888a64f7c2a</a></li> + <li>matchms_metadata_export was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/matchms_metadata_export/7a489b217930">7a489b217930</a></li> + <li>matchms_metadata_match was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/matchms_metadata_match/f72cc5505da3">f72cc5505da3</a></li> + <li>matchms_metadata_merge was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/matchms_metadata_merge/3a37748f6c95">3a37748f6c95</a></li> + <li>matchms_networking was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/matchms_networking/2200e9b7a2b3">2200e9b7a2b3</a></li> + <li>matchms_remove_key was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/matchms_remove_key/ea891750acfc">ea891750acfc</a></li> + <li>matchms_spectral_similarity was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/matchms_spectral_similarity/9782eb7a22b7">9782eb7a22b7</a></li> + <li>matchms_split was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/matchms_split/1dcd8b0bd608">1dcd8b0bd608</a></li> + <li>matchms_subsetting was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/matchms_subsetting/1387786b6206">1387786b6206</a></li> +</ul> + +<h2 id="chemicaltoolbox">ChemicalToolBox</h2> + +<ul> + <li>rem_complex was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/rem_complex/1dc9f5a3163d">1dc9f5a3163d</a></li> +</ul> + +<h2 id="qiime-2">QIIME 2</h2> + +<ul> + <li>qiime2__deblur__denoise_16S was updated to <a href="https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/2572fc0f88f2">2572fc0f88f2</a></li> +</ul> + +<h2 id="proteomics">Proteomics</h2> + +<ul> + <li>openms_openpepxl was updated to <a href="https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_openpepxl/a2a842b00f9c">a2a842b00f9c</a></li> + <li>openms_percolatoradapter was updated to <a href="https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_percolatoradapter/0fc9ae55bcfc">0fc9ae55bcfc</a></li> + <li>openms_percolatoradapter was updated to <a href="https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_percolatoradapter/e7881a82b56d">e7881a82b56d</a></li> + <li>openms_xfdr was updated to <a href="https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_xfdr/81402a5e4173">81402a5e4173</a></li> + <li>openms_xfdr was updated to <a href="https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_xfdr/9a6e3bb0f358">9a6e3bb0f358</a></li> +</ul> + +<h2 id="convert-formats">Convert Formats</h2> + +<ul> + <li>graphicsmagick_image_convert was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/graphicsmagick_image_convert/99217847314a">99217847314a</a></li> + <li>graphicsmagick_image_montage was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/graphicsmagick_image_montage/4dada93ef525">4dada93ef525</a></li> + <li>graphicsmagick_image_montage was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/graphicsmagick_image_montage/a0f01c777820">a0f01c777820</a></li> +</ul> + +<h2 id="imaging">Imaging</h2> + +<ul> + <li>bia_download was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/bia_download/3085096f2b99">3085096f2b99</a></li> +</ul> + +<h2 id="ncbi-blast">NCBI Blast</h2> + +<ul> + <li>magicblast was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/magicblast/79f4f8bd0e34">79f4f8bd0e34</a></li> +</ul> + +<h2 id="phylogenetics">Phylogenetics</h2> + +<ul> + <li>hyphy_prime was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/hyphy_prime/4072360120e4">4072360120e4</a></li> +</ul> + +<h2 id="none">None</h2> + +<ul> + <li>data_manager_diamond_database_builder was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_diamond_database_builder/4a08b7b76b78">4a08b7b76b78</a></li> +</ul> + +<h2 id="rna-analysis">RNA Analysis</h2> + +<ul> + <li>rbpbench was updated to <a href="https://toolshed.g2.bx.psu.edu/view/rnateam/rbpbench/b022c6591515">b022c6591515</a></li> +</ul>On 2023-12-07, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in Jenkins Build #421UseGalaxy.eu Tool Updates for 2023-12-032023-12-03T00:00:00+01:002023-12-03T00:00:00+01:00https://galaxyproject.eu/posts/2023/12/03/tool-update<p>On 2023-12-03, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in <a href="https://build.galaxyproject.eu/job/usegalaxy-eu/job/install-tools/#420/">Jenkins Build #420</a></p> + +<h2 id="filter-and-sort">Filter and Sort</h2> + +<ul> + <li>sample_seqs was updated to <a href="https://toolshed.g2.bx.psu.edu/view/peterjc/sample_seqs/bdaefd241921">bdaefd241921</a></li> + <li>seq_filter_by_id was updated to <a href="https://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id/83a19df00eab">83a19df00eab</a></li> +</ul> + +<h2 id="data-and-metadata-management">Data and Metadata Management</h2> + +<ul> + <li>eml2eal was updated to <a href="https://toolshed.g2.bx.psu.edu/view/ecology/eml2eal/3d14d6a4ef7c">3d14d6a4ef7c</a></li> + <li>makeeml was updated to <a href="https://toolshed.g2.bx.psu.edu/view/ecology/makeeml/8a697f446051">8a697f446051</a></li> +</ul> + +<h2 id="metabolomics">Metabolomics</h2> + +<ul> + <li>matchms_formatter was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/matchms_formatter/86a45ba3d3f2">86a45ba3d3f2</a></li> + <li>matchms_metadata_merge was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/matchms_metadata_merge/caf007467c84">caf007467c84</a></li> + <li>matchms_subsetting was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/matchms_subsetting/aa2e912f9dc2">aa2e912f9dc2</a></li> +</ul> + +<h2 id="qiime-2">QIIME 2</h2> + +<ul> + <li>qiime2__deblur__denoise_16S was updated to <a href="https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/2572fc0f88f2">2572fc0f88f2</a></li> +</ul> + +<h2 id="proteomics">Proteomics</h2> + +<ul> + <li>diann was updated to <a href="https://toolshed.g2.bx.psu.edu/view/galaxyp/diann/bf0728e000cd">bf0728e000cd</a></li> + <li>openms_openpepxl was updated to <a href="https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_openpepxl/40cc19c0dbd6">40cc19c0dbd6</a></li> + <li>openms_openpepxl was updated to <a href="https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_openpepxl/a2a842b00f9c">a2a842b00f9c</a></li> + <li>openms_openpepxl was updated to <a href="https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_openpepxl/fc36cfd19834">fc36cfd19834</a></li> + <li>openms_percolatoradapter was updated to <a href="https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_percolatoradapter/0fc9ae55bcfc">0fc9ae55bcfc</a></li> + <li>openms_percolatoradapter was updated to <a href="https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_percolatoradapter/e7881a82b56d">e7881a82b56d</a></li> + <li>openms_xfdr was updated to <a href="https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_xfdr/81402a5e4173">81402a5e4173</a></li> + <li>openms_xfdr was updated to <a href="https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_xfdr/9a6e3bb0f358">9a6e3bb0f358</a></li> +</ul> + +<h2 id="nanopore">Nanopore</h2> + +<ul> + <li>nanopolish_eventalign was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/nanopolish_eventalign/3b6f94fc7e1d">3b6f94fc7e1d</a></li> + <li>nanopolish_methylation was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/nanopolish_methylation/90a922f32523">90a922f32523</a></li> + <li>nanopolish_polya was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/nanopolish_polya/4857d5bcce52">4857d5bcce52</a></li> + <li>nanopolish_variants was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/nanopolish_variants/bec636361cfd">bec636361cfd</a></li> +</ul> + +<h2 id="assembly">Assembly</h2> + +<ul> + <li>getorganelle was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/getorganelle/7348b69e5109">7348b69e5109</a></li> + <li>megahit was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/megahit/a96f3ad4e0d8">a96f3ad4e0d8</a></li> +</ul> + +<h2 id="phylogenetics">Phylogenetics</h2> + +<ul> + <li>hyphy_prime was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/hyphy_prime/4072360120e4">4072360120e4</a></li> +</ul> + +<h2 id="single-cell">Single-cell</h2> + +<ul> + <li>baredsc_1d was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/baredsc_1d/0e70b2dfe4be">0e70b2dfe4be</a></li> + <li>baredsc_2d was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/baredsc_2d/344c2af50552">344c2af50552</a></li> + <li>baredsc_combine_1d was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/baredsc_combine_1d/b13d3e4c48e1">b13d3e4c48e1</a></li> + <li>baredsc_combine_2d was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/baredsc_combine_2d/1d77986f9ddc">1d77986f9ddc</a></li> +</ul> + +<h2 id="none">None</h2> + +<ul> + <li>data_manager_diamond_database_builder was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_diamond_database_builder/4a08b7b76b78">4a08b7b76b78</a></li> +</ul> + +<h2 id="annotation">Annotation</h2> + +<ul> + <li>braker3 was updated to <a href="https://toolshed.g2.bx.psu.edu/view/genouest/braker3/5460380cc057">5460380cc057</a></li> +</ul> + +<h2 id="spatial-omics">Spatial Omics</h2> + +<ul> + <li>mesmer was updated to <a href="https://toolshed.g2.bx.psu.edu/view/goeckslab/mesmer/c60b810d570d">c60b810d570d</a></li> +</ul> + +<h2 id="fastafastq">FASTA/FASTQ</h2> + +<ul> + <li>seq_filter_by_mapping was updated to <a href="https://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_mapping/566e456371c6">566e456371c6</a></li> +</ul>On 2023-12-03, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in Jenkins Build #420UseGalaxy.eu Tool Updates for 2023-11-262023-11-26T00:00:00+01:002023-11-26T00:00:00+01:00https://galaxyproject.eu/posts/2023/11/26/tool-update<p>On 2023-11-26, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in <a href="https://build.galaxyproject.eu/job/usegalaxy-eu/job/install-tools/#419/">Jenkins Build #419</a></p> <h2 id="metabolomics">Metabolomics</h2> @@ -898,125 +1080,4 @@ <li>scanpy_run_tsne was updated to <a href="https://toolshed.g2.bx.psu.edu/view/ebi-gxa/scanpy_run_tsne/64cd33540fee">64cd33540fee</a></li> <li>scanpy_run_umap was updated to <a href="https://toolshed.g2.bx.psu.edu/view/ebi-gxa/scanpy_run_umap/9984f48961d0">9984f48961d0</a></li> <li>scanpy_scale_data was updated to <a href="https://toolshed.g2.bx.psu.edu/view/ebi-gxa/scanpy_scale_data/bf30bd6355da">bf30bd6355da</a></li> -</ul>On 2023-10-15, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in Jenkins Build #411UseGalaxy.eu Tool Updates for 2023-10-082023-10-08T00:00:00+02:002023-10-08T00:00:00+02:00https://galaxyproject.eu/posts/2023/10/08/tool-update<p>On 2023-10-08, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in <a href="https://build.galaxyproject.eu/job/usegalaxy-eu/job/install-tools/#410/">Jenkins Build #410</a></p> - -<h2 id="metabolomics">Metabolomics</h2> - -<ul> - <li>waveica was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/waveica/6480c6d5fa36">6480c6d5fa36</a></li> -</ul> - -<h2 id="qiime-2">QIIME 2</h2> - -<ul> - <li>qiime2__deblur__denoise_16S was updated to <a href="https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/2572fc0f88f2">2572fc0f88f2</a></li> -</ul> - -<h2 id="proteomics">Proteomics</h2> - -<ul> - <li>diann was updated to <a href="https://toolshed.g2.bx.psu.edu/view/galaxyp/diann/ae4dc0c041f9">ae4dc0c041f9</a></li> - <li>openms_openpepxl was updated to <a href="https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_openpepxl/40cc19c0dbd6">40cc19c0dbd6</a></li> - <li>openms_openpepxl was updated to <a href="https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_openpepxl/a2a842b00f9c">a2a842b00f9c</a></li> - <li>openms_openpepxl was updated to <a href="https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_openpepxl/fc36cfd19834">fc36cfd19834</a></li> - <li>openms_percolatoradapter was updated to <a href="https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_percolatoradapter/0fc9ae55bcfc">0fc9ae55bcfc</a></li> - <li>openms_percolatoradapter was updated to <a href="https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_percolatoradapter/e7881a82b56d">e7881a82b56d</a></li> - <li>openms_xfdr was updated to <a href="https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_xfdr/81402a5e4173">81402a5e4173</a></li> - <li>openms_xfdr was updated to <a href="https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_xfdr/9a6e3bb0f358">9a6e3bb0f358</a></li> -</ul> - -<h2 id="machine-learning">Machine Learning</h2> - -<ul> - <li>sklearn_model_fit was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/sklearn_model_fit/8e447b95e6a8">8e447b95e6a8</a></li> -</ul> - -<h2 id="single-cell">Single-cell</h2> - -<ul> - <li>baredsc_1d was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/baredsc_1d/02b1fe7aed76">02b1fe7aed76</a></li> - <li>baredsc_2d was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/baredsc_2d/c29e7bb492bf">c29e7bb492bf</a></li> - <li>baredsc_combine_1d was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/baredsc_combine_1d/c32347702e12">c32347702e12</a></li> - <li>baredsc_combine_2d was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/baredsc_combine_2d/239193b96d72">239193b96d72</a></li> -</ul> - -<h2 id="variant-calling">Variant Calling</h2> - -<ul> - <li>beacon2_csv2xlsx was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/beacon2_csv2xlsx/ba4ed464f8b6">ba4ed464f8b6</a></li> - <li>beacon2_pxf2bff was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/beacon2_pxf2bff/30605b5fc43f">30605b5fc43f</a></li> - <li>beacon2_vcf2bff was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/beacon2_vcf2bff/0a757835a745">0a757835a745</a></li> - <li>cnvkit_breaks was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_breaks/ef9a50eb20ce">ef9a50eb20ce</a></li> - <li>cnvkit_genemetrics was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_genemetrics/2b53415d4f3c">2b53415d4f3c</a></li> - <li>cnvkit_segmetrics was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_segmetrics/d9cb65e1f756">d9cb65e1f756</a></li> - <li>cnvkit_sex was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_sex/3316bd294f6f">3316bd294f6f</a></li> -</ul> - -<h2 id="virology">Virology</h2> - -<ul> - <li>cooc_mutbamscan was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/cooc_mutbamscan/cd0484c5f9f1">cd0484c5f9f1</a></li> - <li>cooc_pubmut was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/cooc_pubmut/0349d8981030">0349d8981030</a></li> - <li>cooc_tabmut was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/cooc_tabmut/52bd683c6d3f">52bd683c6d3f</a></li> -</ul> - -<h2 id="none">None</h2> - -<ul> - <li>data_manager_diamond_database_builder was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_diamond_database_builder/4a08b7b76b78">4a08b7b76b78</a></li> -</ul>On 2023-10-08, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in Jenkins Build #410UseGalaxy.eu Tool Updates for 2023-10-062023-10-06T00:00:00+02:002023-10-06T00:00:00+02:00https://galaxyproject.eu/posts/2023/10/06/tool-update<p>On 2023-10-06, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in <a href="https://build.galaxyproject.eu/job/usegalaxy-eu/job/install-tools/#409/">Jenkins Build #409</a></p> - -<h2 id="machine-learning">Machine Learning</h2> - -<ul> - <li>keras_model_builder was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/keras_model_builder/20cd4269deb2">20cd4269deb2</a></li> - <li>keras_model_config was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/keras_model_config/b9906ce4756c">b9906ce4756c</a></li> - <li>keras_train_and_eval was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/keras_train_and_eval/e29894cdea47">e29894cdea47</a></li> - <li>sklearn_data_preprocess was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/sklearn_data_preprocess/9e43ee712723">9e43ee712723</a></li> - <li>sklearn_estimator_attributes was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/sklearn_estimator_attributes/adaf2457d6ec">adaf2457d6ec</a></li> - <li>sklearn_fitted_model_eval was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/sklearn_fitted_model_eval/f73a2b68a37b">f73a2b68a37b</a></li> - <li>sklearn_pca was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/sklearn_pca/03e0da430d44">03e0da430d44</a></li> -</ul> - -<h2 id="metabolomics">Metabolomics</h2> - -<ul> - <li>matchms_filtering was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/matchms_filtering/357df6c47d92">357df6c47d92</a></li> - <li>ramclustr was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/ramclustr/2ec9253a647e">2ec9253a647e</a></li> - <li>ramclustr_define_experiment was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/ramclustr_define_experiment/25625114618e">25625114618e</a></li> - <li>waveica was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/waveica/b77023c41c76">b77023c41c76</a></li> -</ul> - -<h2 id="qiime-2">QIIME 2</h2> - -<ul> - <li>qiime2__deblur__denoise_16S was updated to <a href="https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/2572fc0f88f2">2572fc0f88f2</a></li> -</ul> - -<h2 id="chemicaltoolbox">ChemicalToolBox</h2> - -<ul> - <li>biomd_rmsd_clustering was updated to <a href="https://toolshed.g2.bx.psu.edu/view/chemteam/biomd_rmsd_clustering/ee1f38eb220e">ee1f38eb220e</a></li> -</ul> - -<h2 id="proteomics">Proteomics</h2> - -<ul> - <li>openms_openpepxl was updated to <a href="https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_openpepxl/a2a842b00f9c">a2a842b00f9c</a></li> - <li>openms_percolatoradapter was updated to <a href="https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_percolatoradapter/0fc9ae55bcfc">0fc9ae55bcfc</a></li> - <li>openms_percolatoradapter was updated to <a href="https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_percolatoradapter/e7881a82b56d">e7881a82b56d</a></li> - <li>openms_xfdr was updated to <a href="https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_xfdr/81402a5e4173">81402a5e4173</a></li> - <li>openms_xfdr was updated to <a href="https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_xfdr/9a6e3bb0f358">9a6e3bb0f358</a></li> -</ul> - -<h2 id="get-data">Get Data</h2> - -<ul> - <li>ega_download_client was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/ega_download_client/f9db47f68e5e">f9db47f68e5e</a></li> -</ul> - -<h2 id="none">None</h2> - -<ul> - <li>data_manager_diamond_database_builder was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_diamond_database_builder/4a08b7b76b78">4a08b7b76b78</a></li> -</ul>On 2023-10-06, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in Jenkins Build #409 \ No newline at end of file +</ul>On 2023-10-15, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in Jenkins Build #411 \ No newline at end of file diff --git a/freiburg/galaxy/gxnews.html b/freiburg/galaxy/gxnews.html index 73624d1eb..61e7c0f11 100644 --- a/freiburg/galaxy/gxnews.html +++ b/freiburg/galaxy/gxnews.html @@ -48,6 +48,138 @@ + tags.push(`tools`) + + tags.push(`Freiburg`) + + if (!userTag ? true : tags.includes(userTag)) { + counter++ + + div = ` + ${counter === 3 ? '
    ' : ''} +
    +
    +
    + + + +

    UseGalaxy.eu Tool Updates for 2023-12-07

    +     + + + + + + + + + + + + + + + + + + December 7, 2023 + + + Freiburg + + + + tools + + + +
    +
    +

    On 2023-12-07, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in Jenkins Build #421

    +
    +
    +
    +
    + ${counter === 3 ? '
    ' : ''} + ` + if (counter === 3) { + counter = 0 + } + + news.append(div); + } + tags = [] + + + + tags.push(`tools`) + + tags.push(`Freiburg`) + + if (!userTag ? true : tags.includes(userTag)) { + counter++ + + div = ` + ${counter === 3 ? '
    ' : ''} +
    +
    +
    + + + +

    UseGalaxy.eu Tool Updates for 2023-12-03

    +     + + + + + + + + + + + + + + + + + + December 3, 2023 + + + Freiburg + + + + tools + + + +
    +
    +

    On 2023-12-03, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in Jenkins Build #420

    +
    +
    +
    +
    + ${counter === 3 ? '
    ' : ''} + ` + if (counter === 3) { + counter = 0 + } + + news.append(div); + } + tags = [] + + + tags.push(`tools`) tags.push(`Freiburg`) diff --git a/freiburg/galaxy/index.html b/freiburg/galaxy/index.html index 0f89e081a..736a39006 100644 --- a/freiburg/galaxy/index.html +++ b/freiburg/galaxy/index.html @@ -55,9 +55,9 @@

    News

    - + -

    Nov 26, 2023

    +

    Dec 7, 2023

    @@ -73,15 +73,15 @@

    - UseGalaxy.eu Tool Updates for 2023-11-26 + UseGalaxy.eu Tool Updates for 2023-12-07

    - + -

    Nov 19, 2023

    +

    Dec 3, 2023

    @@ -97,15 +97,15 @@

    - UseGalaxy.eu Tool Updates for 2023-11-19 + UseGalaxy.eu Tool Updates for 2023-12-03

    - + -

    Nov 14, 2023

    +

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    @@ -121,15 +121,15 @@

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    On 2023-12-07, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in Jenkins Build #421

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    Supported by

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    European Galaxy tools (3305 and counting)

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    Nov 26, 2023

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    Dec 7, 2023

    @@ -62,15 +62,15 @@

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    Nov 19, 2023

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    Dec 3, 2023

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    Nov 12, 2023

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    Nov 19, 2023

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    Oct 29, 2023

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    Nov 12, 2023

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