Difference between revisions of "Template:Article of the week"

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<div style="float: left; margin: 0.5em 0.9em 0.4em 0em;">[[File:GA Karim JofKSUScience2022 34-2.jpg|240px]]</div>
<div style="float: left; margin: 0.5em 0.9em 0.4em 0em;">[[File:GA Terlouw JofCheminfo22 14.png|240px]]</div>
'''"[[Journal:Development of Biosearch System for biobank management and storage of disease-associated genetic information|Development of Biosearch System for biobank management and storage of disease-associated genetic information]]"'''
'''"[[Journal:PIKAChU: A Python-based informatics kit for analyzing chemical units|PIKAChU: A Python-based informatics kit for analyzing chemical units]]"'''


Databases and software are important to manage modern high-throughput [[Laboratory|laboratories]] and store clinical and [[Genome informatics|genomic information]] for [[quality assurance]]. Commercial software is expensive, with proprietary code issues, while academic versions have adaptation issues. Our aim was to develop an adaptable in-house software system that can store specimen- and disease-associated genetic information in [[biobank]]s to facilitate [[translational research]]. A prototype was designed per the research requirements, and computational tools were used to develop the software under three tiers, using Visual Basic and ASP.net for the presentation tier, SQL Server for the data tier, and Ajax and JavaScript for the business tier. We retrieved specimens from the biobank using this software and performed microarray-based transcriptomic analysis to detect differentially expressed genes (DEGs) ... ('''[[Journal:Development of Biosearch System for biobank management and storage of disease-associated genetic information|Full article...]]''')<br />
As efforts to computationally describe and simulate the biochemical world become more commonplace, computer programs that are capable of ''in silico'' chemistry play an increasingly important role in biochemical research. While such programs exist, they are often dependency-heavy, difficult to navigate, or not written in [[Python (programming language)|Python]], the programming language of choice for [[Bioinformatics|bioinformaticians]]. Here, we introduce PIKAChU (Python-based Informatics Kit for Analysing CHemical Units), a [[Chemical informatics|cheminformatics]] toolbox with few dependencies implemented in Python. PIKAChU builds comprehensive molecular graphs from simplified molecular-input line-entry system (SMILES) strings, which allow for easy downstream analysis and visualization of molecules. ... ('''[[Journal:PIKAChU: A Python-based informatics kit for analyzing chemical units|Full article...]]''')<br />
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''Recently featured'':
''Recently featured'':
{{flowlist |
{{flowlist |
* [[Journal:Development of Biosearch System for biobank management and storage of disease-associated genetic information|Development of Biosearch System for biobank management and storage of disease-associated genetic information]]
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}}
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Revision as of 15:55, 20 March 2023

GA Terlouw JofCheminfo22 14.png

"PIKAChU: A Python-based informatics kit for analyzing chemical units"

As efforts to computationally describe and simulate the biochemical world become more commonplace, computer programs that are capable of in silico chemistry play an increasingly important role in biochemical research. While such programs exist, they are often dependency-heavy, difficult to navigate, or not written in Python, the programming language of choice for bioinformaticians. Here, we introduce PIKAChU (Python-based Informatics Kit for Analysing CHemical Units), a cheminformatics toolbox with few dependencies implemented in Python. PIKAChU builds comprehensive molecular graphs from simplified molecular-input line-entry system (SMILES) strings, which allow for easy downstream analysis and visualization of molecules. ... (Full article...)

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