Best Claude prompts for Biological Scientists, All Other

Given a set of Illumina paired-end reads from a newly sequenced genome, design an optimized genome assembly pipeline using a combination of k-mer based and overlap-layout-consensus approaches. The pipeline should include quality control checks, adapter trimming, and scaffolding using a reference genome. Provide a detailed command-line workflow using tools such as FastQC, Trimmomatic, and SPAdes, and estimate the computational resources required to complete the assembly within a 2-week timeframe.

Reconstruct a phylogenetic tree from a set of protein-coding gene sequences using a maximum likelihood approach, and analyze the resulting tree to identify patterns of molecular evolution and potential gene flow between different species. Use tools such as RAxML and FigTree to generate the tree and visualize the results, and provide a detailed interpretation of the tree topology and branch lengths in the context of the underlying biology.

Develop a computational model of a cellular signaling network using a combination of ordinary differential equations and stochastic simulation approaches. The model should include key regulatory components such as protein kinases, phosphatases, and transcription factors, and should be able to simulate the dynamic behavior of the network in response to different stimuli. Use tools such as COPASI and CellDesigner to implement the model and analyze the results, and provide a detailed interpretation of the simulation outputs in the context of the underlying biology.

Analyze a set of gene expression microarray data from a recently published study to identify key regulatory modules and predict potential transcriptional regulators. Use tools such as WGCNA and Cytoscape to generate co-expression networks and visualize the results, and provide a detailed interpretation of the network topology and module assignments in the context of the underlying biology. Also, use tools such as MEME and JASPAR to predict potential transcription factor binding sites and validate the results using experimental data from the literature.