Details

Autor(en) / Beteiligte

• Via, Allegra
• Rother, Kristian
• Tramontano, Anna

Titel

Managing Your Biological Data with Python

Auflage

1

Ort / Verlag

London: CRC Press LLC

Erscheinungsjahr

2014

Link zum Volltext

Quelle

Alma/SFX Local Collection

Beschreibungen/Notizen

• Getting StartedThe Python Shell In This Chapter You Will Learn Story: Calculating the ΔG of ATP Hydrolysis What Do the Commands Mean? Examples Testing Yourself Your First Python Program In This Chapter You Will Learn Story: How to Calculate the Frequency of Amino Acids from InsulinWhat Do the Commands Mean? Examples Testing Yourself Data ManagementAnalyzing a Data Column In This Chapter You Will Learn Story: Dendritic Lengths What Do the Commands Mean? Examples Testing Yourself Parsing Data Records In This Chapter You Will Learn Story: Integrating Mass Spectrometry Data into Metabolic PathwaysWhat Do the Commands Mean? Examples Testing Yourself Searching DataIn This Chapter You Will Learn Story: Translating an RNA Sequence into the Corresponding Protein SequenceWhat Do the Commands Mean? Examples Testing Yourself Filtering DataIn This Chapter You Will Learn Story: Working with RNA-Seq Output DataWhat Do the Commands Mean? Examples Testing Yourself Managing Tabular DataIn This Chapter You Will Learn Story: Determining Protein ConcentrationsWhat Do the Commands Mean? Examples Testing Yourself Sorting DataIn This Chapter You Will Learn Story: Sort a Data TableWhat Do the Commands Mean? Examples Testing Yourself Pattern Matching and Text MiningIn This Chapter You Will Learn Story: Search a Phosphorylation Motif in a Protein SequenceWhat Do the Commands Mean? Examples Testing Yourself Modular ProgrammingDivide a Program into FunctionsIn This Chapter You Will Learn Story: Working with Three-Dimensional Coordinate FilesWhat Do the Commands Mean? Examples Testing Yourself Managing Complexity with ClassesIn This Chapter You Will Learn Story: Mendelian InheritanceWhat Do the Commands Mean? Examples Testing Yourself DebuggingIn This Chapter You Will Learn Story: When Your Program Does Not WorkWhat Do the Commands Mean? Examples Testing Yourself Using External Modules: The Python Interface to RIn This Chapter You Will Learn Story: Reading Numbers from a File and Calculating Their Mean Value Using R with PythonWhat Do the Commands Mean? Examples Testing Yourself Building Program PipelinesIn This Chapter You Will Learn Story: Building an NGS PipelineWhat Do the Commands Mean? Examples Testing Yourself Writing Good ProgramsIn This Chapter You Will Learn Problem Description: UncertaintyWhat Do the Commands Mean? Examples Testing Yourself Data VisualizationCreating Scientific DiagramsIn This Chapter You Will Learn Story: Nucleotide Frequencies in the RibosomeWhat Do the Commands Mean? Examples Testing Yourself Creating Molecule Images with PyMOLIn This Chapter You Will Learn Story: The Zinc FingerSeven Steps to Create a High-Resolution ImageExamples Testing Yourself Manipulating ImagesIn This Chapter You Will Learn Story: Plot a PlasmidWhat Do the Commands Mean? Examples Testing Yourself BiopythonWorking with Sequence DataIn This Chapter You Will Learn Story: How to Translate a DNA Coding Sequence into the Corresponding Protein Sequence and Write It to a FASTA FileWhat Do the Commands Mean? Examples Testing Yourself Retrieving Data from Web ResourcesIn This Chapter You Will Learn Story: Searching Publications by Keywords in PubMed, Downloading the Corresponding Records, and Writing Papers Published in a Given Year to a FileWhat Do the Commands Mean? Examples Testing Yourself Working with 3D Structure DataIn This Chapter You Will Learn Story: Extracting Atom Names and Three-Dimensional Coordinates from a PDB FileWhat Do the Commands Mean? Examples Testing Yourself CookbookRecipe 1: The PyCogent Library Recipe 2: Reversing and Randomizing a SequenceRecipe 3: Creating a Random Sequence with Probabilities Recipe 4: Parsing Multiple Sequence Alignments Using Biopython Recipe 5: Calculating a Consensus Sequence from a Multiple Sequence Alignment Recipe 6: Calculating the Distance between Phylogenetic Tree Nodes Recipe 7: Codon Frequencies in a Nucleotide Sequence Recipe 8: Parsing RNA 2D Structures in the Vienna FormatRecipe 9: Parsing BLAST XML OutputRecipe 10: Parsing SBML Files Recipe 11: Running BLAST Recipe 12: Accessing, Downloading, and Reading Web Pages in Python Recipe 13: Parsing HTML Files Recipe 14: Split a PDB File into PDB Chain Files Recipe 15: Find the Two Closest Cα Atoms in a PDB Structure Recipe 16: Extract the Interface between Two PDB ChainsRecipe 17: Building Homology Models Using Modeller Recipe 18: RNA 3D Homology Modeling with ModeRNA Recipe 19: Calculating RNA Base Pairs from a 3D Structure Recipe 20: A Real Case of Structural Superimposition: The Serine Protease Catalytic Triad Appendix A: Command OverviewAppendix B: Python ResourcesAppendix C: Record SamplesAppendix D: Handling Directories and Programs with UNIX.