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Python is a free and powerful tool which can be used to build a financial calculator and price options, and can also explain many trading strategies and test various hypotheses. In addition to that, real-world data can be used to run CAPM (Capital Asset Pricing Model), the Fama-French 3-factor model, estimate VaR (Value at Risk), and estimate spread, illiquidity, and liquidity. This book explores the basics of programming in Python. It is a step-by-step tutorial that will teach you, with the help of concise, practical programs, how to run various statistic tests. With this book, you will learn how to implement financial concepts using python libraries like NumPy, SciPy and Matplotlib. This book introduces you to the basic concepts and operations related to Python. After that, we move on to how you can use Python to build a financial calculator. After going through several key modules (packages), you will learn how to run various statistics tests such as T-tests, F-tests, and normality tests. The book will then cover how to run CAPM (Capital Asset Pricing Model) and the Fama-French 3-factor model, as well as how to form various portfolios and estimate individual stock and portfolios' VaR (Value at Risk). You will learn about various financial concepts using python libraries like NumPy, SciPy and Matplotlib, and trading strategies through illustrations and graphs. You will also learn how to retrieve the historical trading data of stock, option data, and other data from public data sources. You will then discover how you can process the data sources that you obtain to estimate returns and convert daily returns into monthly or annual returns, as well as how to estimate a portfolio's variance-covariance matrix. A hands-on guide with easy-to-follow examples to help you learn about option theory, quantitative finance, financial modeling, and time series using Python. Python for Finance is perfect for graduate students, practitioners, and application developers who wish to learn how to utilize Python to handle their financial needs. Basic knowledge of Python will be helpful but knowledge of programming is necessary.

Python is a free and powerful tool that can be used to build a financial calculator and price options, and can also explain many trading strategies and test various hypotheses. This book details the steps needed to retrieve time series data from differ

The use of computation and simulation has become an essential part of the scientific process. Being able to transform a theory into an algorithm requires significant theoretical insight, detailed physical and mathematical understanding, and a working level of competency in programming. This upper-division text provides an unusually broad survey of the topics of modern computational physics from a multidisciplinary, computational science point of view. Its philosophy is rooted in learning by doing (assisted by many model programs), with new scientific materials as well as with the Python programming language. Python has become very popular, particularly for physics education and large scientific projects. It is probably the easiest programming language to learn for beginners, yet is also used for mainstream scientific computing, and has packages for excellent graphics and even symbolic manipulations. The text is designed for an upper-level undergraduate or beginning graduate course and provides the reader with the essential knowledge to understand computational tools and mathematical methods well enough to be successful. As part of the teaching of using computers to solve scientific problems, the reader is encouraged to work through a sample problem stated at the beginning of each chapter or unit, which involves studying the text, writing, debugging and running programs, visualizing the results, and the expressing in words what has been done and what can be concluded. Then there are exercises and problems at the end of each chapter for the reader to work on their own (with model programs given for that purpose).  

This book will teach you to use Python and the Python Data Analysis Library (pandas) to solve real-world financial problems. Starting with a focus on pandas data structures, you will learn to load and manipulate time-series financial data and then calculate common financial measures, leading into more advanced derivations using fixed- and moving-windows. This leads into correlating time-series data to both index and social data to build simple trading algorithms. From there, you will learn about more complex trading algorithms and implement them using open source back-testing tools. Then, you will examine the calculation of the value of options and Value at Risk. This then leads into the modeling of portfolios and calculation of optimal portfolios based upon risk. All concepts will be demonstrated continuously through progressive examples using interactive Python and IPython Notebook. By the end of the book, you will be familiar with applying pandas to many financial problems, giving you the knowledge needed to leverage pandas in the real world of finance.

Background Biotite is a program library for sequence and structural bioinformatics written for the Python programming language. It implements widely used computational methods into a consistent and accessible package. This allows for easy combination of various data analysis, modeling and simulation methods. Results This article presents major functionalities introduced into Biotite since its original publication. The fields of application are shown using concrete examples. We show that the computational performance of Biotite for bioinformatics tasks is comparable to individual, special purpose software systems specifically developed for the respective single task. Conclusions The results show that Biotite can be used as program library to either answer specific bioinformatics questions and simultaneously allow the user to write entire, self-contained software applications with sufficient performance for general application.

Background Even though several computational methods for rhythmicity detection and analysis of biological data have been proposed in recent years, classical trigonometric regression based on cosinor still has several advantages over these methods and is still widely used. Different software packages for cosinor-based rhythmometry exist, but lack certain functionalities and require data in different, non-unified input formats. Results We present CosinorPy, a Python implementation of cosinor-based methods for rhythmicity detection and analysis. CosinorPy merges and extends the functionalities of existing cosinor packages. It supports the analysis of rhythmic data using single- or multi-component cosinor models, automatic selection of the best model, population-mean cosinor regression, and differential rhythmicity assessment. Moreover, it implements functions that can be used in a design of experiments, a synthetic data generator, and import and export of data in different formats. Conclusion CosinorPy is an easy-to-use Python package for straightforward detection and analysis of rhythmicity requiring minimal statistical knowledge, and produces publication-ready figures. Its code, examples, and documentation are available to download from https://github.com/mmoskon/CosinorPy . CosinorPy can be installed manually or by using pip, the package manager for Python packages. The implementation reported in this paper corresponds to the software release v1.1.

Background Computational mathematical models of biological and biomedical systems have been successfully applied to advance our understanding of various regulatory processes, metabolic fluxes, effects of drug therapies, and disease evolution and transmission. Unfortunately, despite community efforts leading to the development of SBML and the BioModels database, many published models have not been fully exploited, largely due to a lack of proper documentation or the dependence on proprietary software. To facilitate the reuse and further development of systems biology and systems medicine models, an open-source toolbox that makes the overall process of model construction more consistent, understandable, transparent, and reproducible is desired. Results and discussion We provide an update on the development of modelbase , a free, expandable Python package for constructing and analysing ordinary differential equation-based mathematical models of dynamic systems. It provides intuitive and unified methods to construct and solve these systems. Significantly expanded visualisation methods allow for convenient analysis of the structural and dynamic properties of models. After specifying reaction stoichiometries and rate equations modelbase can automatically assemble the associated system of differential equations. A newly provided library of common kinetic rate laws reduces the repetitiveness of the computer programming code. modelbase  is also fully compatible with SBML. Previous versions provided functions for the automatic construction of networks for isotope labelling studies. Now, using user-provided label maps, modelbase  v1.2.3 streamlines the expansion of classic models to their isotope-specific versions. Finally, the library of previously published models implemented in modelbase  is growing continuously. Ranging from photosynthesis to tumour cell growth to viral infection evolution, all these models are now available in a transparent, reusable and unified format through  modelbase . Conclusion With this new Python software package, which is written in currently one of the most popular programming languages, the user can develop new models and actively profit from the work of others. modelbase  enables reproducing and replicating models in a consistent, tractable and expandable manner. Moreover, the expansion of models to their isotopic label-specific versions enables simulating label propagation, thus providing quantitative information regarding network topology and metabolic fluxes.

Biochemical signaling pathways in living cells are often highly organized into spatially segregated volumes, membranes, scaffolds, subcellular compartments, and organelles comprising small numbers of interacting molecules. At this level of granularity stochastic behavior dominates, well-mixed continuum approximations based on concentrations break down and a particle-based approach is more accurate and more efficient. We describe and validate a new version of the open-source MCell simulation program (MCell4), which supports generalized 3D Monte Carlo modeling of diffusion and chemical reaction of discrete molecules and macromolecular complexes in solution, on surfaces representing membranes, and combinations thereof. The main improvements in MCell4 compared to the previous versions, MCell3 and MCell3-R, include a Python interface and native BioNetGen reaction language (BNGL) support. MCell4’s Python interface opens up completely new possibilities for interfacing with external simulators to allow creation of sophisticated event-driven multiscale/multiphysics simulations. The native BNGL support, implemented through a new open-source library libBNG (also introduced in this paper), provides the capability to run a given BNGL model spatially resolved in MCell4 and, with appropriate simplifying assumptions, also in the BioNetGen simulation environment, greatly accelerating and simplifying model validation and comparison.