Appyters: Turning Jupyter Notebooks into data-driven web apps

Clarke, Daniel J B; Jeon, Minji; Stein, Daniel J.; Moiseyev, Nicole; Kropiwnicki, Eryk; Dai, Charles; Xie, Zhuorui; Wojciechowicz, Megan L.; Litz, Skylar; Hom, Jason; Evangelista, John Erol; Goldman, Lucas; Zhang, Serena; Yoon, Christine; Ahamed, Tahmid; Bhuiyan, Samantha; Cheng, Minxuan; Karam, Julie; Jagodnik, Kathleen M.; Shu, Ingrid; Lachmann, Alexander; Ayling, Sam; Jenkins, Sherry L.; Ma’ayan, Avi

doi:10.1016/j.patter.2021.100213

Cited by 78 publications

(71 citation statements)

References 65 publications

(82 reference statements)

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“…Gene expression data from TCGA and CGGA datasets was downloaded as raw counts and processed using the online tool Appyter [ 19 , 20 , 45 ]. DEGs between IDH wt/mut gliomas were generated using the Limma package with a p-value cutoff of 0.05 and a fold change cutoff of 0.2.…”

Section: Methodsmentioning

confidence: 99%

IDH1 mutant glioma is preferentially sensitive to the HDAC inhibitor panobinostat

2021

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Introduction A large subset of diffusely infiltrative gliomas contains a gain-of-function mutation in isocitrate dehydrogenase 1 or 2 (IDH1/2mut) which produces 2-hydroxglutarate, an inhibitor of α-ketoglutarate-dependent DNA demethylases, thereby inducing widespread DNA and histone methylation. Because histone deacetylase (HDAC) enzymes are localized to methylated chromatin via methyl-binding domain proteins, IDH1/2mut gliomas may be more dependent on HDAC activity, and therefore may be more sensitive to HDAC inhibitors. Methods Six cultured patient-derived glioma cell lines, IDH1wt (n = 3) and IDH1mut (n = 3), were treated with an FDA-approved HDAC inhibitor, panobinostat. Cellular cytotoxicity and proliferation assays were conducted by flow cytometry. Histone modifications and cell signaling pathways were assessed using immunoblot and/or ELISA. Results IDH1mut gliomas exhibited marked upregulation of genes associated with the HDAC activity. Glioma cell cultures bearing IDH1mut were significantly more sensitive to the cytotoxic and antiproliferative effects of panobinostat, compared to IDH1wt glioma cells. Panobinostat caused a greater increase in acetylation of the histone residues H3K14, H3K18, and H3K27 in IDH1mut glioma cells. Another HDAC inhibitor, valproic acid, was also more effective against IDH1mut glioma cells. Conclusion These data suggest that IDH1mut gliomas may be preferentially sensitive to HDAC inhibitors. Further, IDH1mut glioma cultures showed enhanced accumulation of acetylated histone residues in response to panobinostat treatment, suggesting a direct epigenetic mechanism for this sensitivity. This provides a rationale for further exploration of HDAC inhibitors against IDH1mut gliomas.

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Section: Methodsmentioning

confidence: 99%

IDH1 mutant glioma is preferentially sensitive to the HDAC inhibitor panobinostat

2021

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“…For gene set enrichment analysis, Enrichr gene set enrichment analysis web server was utilized [ 18 ]. Visualization for enrichment analysis was performed with the Appyters [ 19 ] programmatically run from the Enrichr results page with default settings for the Enrichr library KEGG 2019 Mouse.…”

Section: Methodsmentioning

confidence: 99%

Intestinal Organoids in Colitis Research: Focusing on Variability and Cryopreservation

Bruegge

Liese

Donath

et al. 2021

Stem Cells International

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In recent years, stem cell-derived organoids have become a cell culture standard that is widely used for studying various scientific issues that were previously investigated through animal experiments and using common tumor cell lines. After their initial hype, concerns regarding their standardization have been raised. Here, we aim to provide some insights into our experience in standardizing murine colonic epithelial organoids, which we use as a replacement method for research on inflammatory bowel disease. Considering good scientific practice, we examined various factors that might challenge the design and outcome of experiments using these organoids. First, to analyze the impact of antibiotics/antimycotics, we performed kinetic experiments using ZellShield® and measured the gene expression levels of the tight junction markers Ocln, Zo-1, and Cldn4, the proliferation marker Ki67, and the proinflammatory cytokine Tnfα. Because we found no differences between cultivations with and without ZellShield®, we then performed infection experiments using the probiotic Escherichia coli Nissle 1917 as an already established model setup to analyze the impact of technical, interexperimental, and biologic replicates. We demonstrate that interexperimental differences pose the greatest challenge for reproducibility and explain our strategies for addressing these differences. Additionally, we conducted infection experiments using freshly isolated and cryopreserved/thawed organoids and found that cryopreservation influenced the experimental outcome during early passages. Formerly cryopreserved colonoids exhibited a premature appearance and a higher proinflammatory response to bacterial stimulation. Therefore, we recommend analyzing the growth characteristics and reliability of cryopreserved organoids before to their use in experiments together with conducting several independent experiments under standardized conditions. Taken together, our findings demonstrate that organoid culture, if standardized, constitutes a good tool for reducing the need for animal experiments and might further improve our understanding of, for example, the role of epithelial cells in inflammatory bowel disease development.

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“…Atualmente, existem trabalhos em andamento para tornar notebooks mais reativos e interativos, assim como planilhas de cálculo [Perkel 2021a]. Outra frente de trabalho busca transformar notebooks em aplicativos Web que sejam leves, interativos, de código aberto e reprodutíveis [Clarke et al 2021]. Os chamados Appyters constituem workflows reutilizáveis baseados na Web e incluem pipelines de aprendizado de máquina, entre outras funções destinadas às áreas de biomedicina e bioinformática.…”

Section: Considerações Finaisunclassified

Ciência de Dados com Reprodutibilidade usando Jupyter

Pimentel¹,

Oliveira²,

Silva³

et al. 2021

Jornada De Atualização Em Informática 2021

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Data Science has become a trending research topic in Computer Science due to the growing interest in extracting knowledge from different data sources. In such a context, Jupyter Notebook has consolidated itself as one of the main tools used by data scientists to perform exploratory data analysis in a fast and straightforward way, with a high potential for code reproduction. Hence, this JAI aims to present Jupyter with reproducibility for developing Data Science projects. The content is tailored for students and professionals with some programming experience. In particular, we first introduce Jupyter and its general use to develop solutions for Data Science. Then, we present Jupyter advanced topics and address ways to promote open science. Finally, this JAI overviews Data Science with Jupyter Notebooks by combining concepts and theoretical foundations with practical examples and real-world data. ResumoCiência de Dados tornou-se um tópico de pesquisa emergente na Ciência da Computação devido ao crescente interesse em extrair conhecimento de diferentes fontes de dados. Nesse contexto, o Jupyter Notebook vem se consolidando como uma das principais ferramentas utilizadas por cientistas de dados para realizar análises exploratórias de dados de forma rápida e direta, com alto potencial de reprodução de código. Dessa forma, o objetivo deste capítulo é apresentar o Jupyter com reprodutibilidade para a realização de projetos em Ciência de Dados. O conteúdo é organizado para estudantes e profissionais com alguma experiência em programação. Em particular, primeiro apresentamos o Jupyter e seu uso geral para desenvolver soluções para Ciência de Dados. Em seguida, apresentamos tópicos avançados do Jupyter e abordamos maneiras de promover a ciência aberta. Para concluir, este JAI apresenta uma visão geral de Ciência de Dados com Jupyter Notebooks combinando conceitos e fundamentos teóricos com exemplos práticos e dados do mundo real.

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Appyters: Turning Jupyter Notebooks into data-driven web apps

Cited by 78 publications

References 65 publications

IDH1 mutant glioma is preferentially sensitive to the HDAC inhibitor panobinostat

IDH1 mutant glioma is preferentially sensitive to the HDAC inhibitor panobinostat

Intestinal Organoids in Colitis Research: Focusing on Variability and Cryopreservation

Ciência de Dados com Reprodutibilidade usando Jupyter

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