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1. Exploring FlyBase Data Using QuickSearch

   https://doi.org/10.1002/cpz1.731  

   Marygold, Steven J. ; the FlyBase Consortium ( April 2023 , Current Protocols)

   FlyBase (www.flybase.org) is the primary online database of genetic, genomic, and functional information aboutDrosophila melanogaster. The long and rich history ofDrosophilaresearch, combined with recent surges in genomic‐scale and high‐throughput technologies, means that FlyBase now houses a huge quantity of data. Researchers need to be able to query these data rapidly and intuitively, and the QuickSearch tool has been designed to meet these needs. This tool is conveniently located on the FlyBase homepage and is organized into a series of simple tabbed interfaces that cover the major data and annotation classes within the database. This article describes the functionality of all aspects of the QuickSearch tool. With this knowledge, FlyBase users will be equipped to take full advantage of all QuickSearch features and thereby gain improved access to data relevant to their research. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC.

   Basic Protocol 1: Using the “Search FlyBase” tab of QuickSearch

   Basic Protocol 2: Using the “Data Class” tab of QuickSearch

   Basic Protocol 3: Using the “References” tab of QuickSearch

   Basic Protocol 4: Using the “Gene Groups” tab of QuickSearch

   Basic Protocol 5: Using the “Pathways” tab of QuickSearch

   Basic Protocol 6: Using the “GO” tab of QuickSearch

   Basic Protocol 7: Using the “Protein Domains” tab of QuickSearch

   Basic Protocol 8: Using the “Expression” tab of QuickSearch

   Basic Protocol 9: Using the “GAL4 etc” tab of QuickSearch

   Basic Protocol 10: Using the “Phenotype” tab of QuickSearch

   Basic Protocol 11: Using the “Human Disease” tab of QuickSearch

   Basic Protocol 12: Using the “Homologs” tab of QuickSearch

   Support Protocol 1: Managing FlyBase hit lists

    

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2. Active Learning a Convex Body in Low Dimensions

   Har-Peled, Sariel ; Jones, Mitchell ; Saladi, Rahul ( July 2020 , Leibniz international proceedings in informatics)

   Czumaj, Artur ; Dawar, Anuj ; Merelli, Emanuela (Ed.)

   Consider a set P ⊆ ℝ^d of n points, and a convex body C provided via a separation oracle. The task at hand is to decide for each point of P if it is in C using the fewest number of oracle queries. We show that one can solve this problem in two and three dimensions using O(⬡_P log n) queries, where ⬡_P is the largest subset of points of P in convex position. In 2D, we provide an algorithm which efficiently generates these adaptive queries. Furthermore, we show that in two dimensions one can solve this problem using O(⊚(P,C) log² n) oracle queries, where ⊚(P,C) is a lower bound on the minimum number of queries that any algorithm for this specific instance requires. Finally, we consider other variations on the problem, such as using the fewest number of queries to decide if C contains all points of P. As an application of the above, we show that the discrete geometric median of a point set P in ℝ² can be computed in O(n log² n (log n log log n + ⬡(P))) expected time. 

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3. Revisiting the driving force inducing phase separation in PEG-phosphate aqueous biphasic systems

   https://doi.org/10.1039/D4FD00058G  

   Bonnassieux, Sophie ; Pandya, Raj ; Adan Skiba, Dhyllan ; Degoulange, Damien ; Petit, Dorothee ; Seem, Peter ; Cowburn, Russell ; Gallant, Betar M ; Grimaud, Alexis Jules ( January 2024 , Faraday Discussions)

   Liquid phase separation using aqueous biphasic systems (ABS) is widely used in industrial processes for the extraction, separation and purification of macromolecules. Using water as the single solvent, a wide...

    

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4. Bulk Acyclic Diene Metathesis Polycondensation

   https://doi.org/10.1002/macp.201900223  

   Bell, Michael ; Hester, Holley Grace ; Gallman, Alec Nicholas ; Gomez, Valentina ; Pribyl, Julia ; Rojas, Giovanni ; Riegger, Andreas ; Weil, Tanja ; Watanabe, Hiro ; Chujo, Yoshiki ; et al ( July 2019 , Macromolecular Chemistry and Physics)

   Bulk acyclic diene metathesis (ADMET) polymerization performed in the melt at temperatures up to 175 °C is completed using a cyclic (alkyl)(amino) carbene (CAAC) ruthenium‐based Grubbs catalyst. High temperature stability is investigated at temperatures well above conventional ADMET chemistry, leading to the highest weight‐average molecular weights ever achieved for any ADMET polymer. A study of isomerization tendency (double bond migration) is done via self‐metathesis of a small molecule model compound using CAAC catalysts. Minimal olefin isomerization is observed using appropriate catalyst ratios and temperatures.

    

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5. MetaMutationalSigs: comparison of mutational signature refitting results made easy

   https://doi.org/10.1093/bioinformatics/btac091  

   Pandey, Palash ; Arora, Sanjeevani ; Rosen, Gail L. ; Marschall, ed., Tobias ( February 2022 , Bioinformatics)

   The analysis of mutational signatures is becoming increasingly common in cancer genetics, with emerging implications in cancer evolution, classification, treatment decision and prognosis. Recently, several packages have been developed for mutational signature analysis, with each using different methodology and yielding significantly different results. Because of the non-trivial differences in tools’ refitting results, researchers may desire to survey and compare the available tools, in order to objectively evaluate the results for their specific research question, such as which mutational signatures are prevalent in different cancer types.

   Due to the need for effective comparison of refitting mutational signatures, we introduce a user-friendly software that can aggregate and visually present results from different refitting packages.

   MetaMutationalSigs is implemented using R and python and is available for installation using Docker and available at: https://github.com/EESI/MetaMutationalSigs.

    

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