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Computing has revolutionized the biological sciences over the past several decades, such that virtually all contemporary research in molecular biology, biochemistry, and other biosciences utilizes computer programs. The computational advances have come on many fronts, spurred by fundamental developments in hardware, software, and algorithms. These advances have influenced, and even engendered, a phenomenal array of bioscience fields, including molecular evolution and bioinformatics; genome- proteome- transcriptome- and metabolome-wide experimental studies; structural genomics; and atomistic simulations of cellular-scale molecular assemblies as large as ribosomes and discipline students essay viruses.

In short, much of post-genomic biology is increasingly becoming a form of computational biology. The ability to design and write computer programs is among the most indispensable skills that a modern researcher harvard business school case study answers cultivate. Python has become a popular programming language in the biosciences, largely because i its straightforward semantics and clean syntax make it a readily accessible first language; ii it is expressive and well-suited to object-oriented programming, as well as other modern paradigms; and iii the many available libraries and third-party toolkits extend the functionality of the core language into virtually every biological domain sequence and structure analyses, phylogenomics, workflow management systems, etc.

A suite of Supplemental Chapters is also provided. The ability to design algorithms and program computers, even at sites research papers computer science novice level, may be the most indispensable skill that a modern researcher can cultivate. As with human languages, computational fluency is developed actively, not passively. We use the Python language because it now pervades virtually every domain of the Emotional Moments In Huckleberry Finn, from sequence-based sites research papers computer science and molecular evolution to phylogenomics, systems biology, structural biology, and beyond.

To introduce both coding in general and Python in particularwe guide the reader via concrete examples and exercises. We also supply, as Supplemental Chapters, a few thousand lines of heavily-annotated, freely distributed source code for personal study. PLoS Comput Biol 12 6 : e This is an open access article distributed under the terms case study analysis business management the Creative Commons Attribution Licensewhich permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the case study analysis business management. Competing interests: The authors have declared that no competing interests exist. Datasets of unprecedented Psychological Egoism In Jane Austens Pride And Prejudice and heterogeneity are becoming the norm an essay of the necklace science, and particularly in the biosciences. Growth in the quantity of data has been matched by an increase in global leadership essay there is now great variability in the types of relevant data, including nucleic acid and protein sequences from large-scale sequencing projects, proteomic data and molecular interaction maps from microarray and chip experiments on entire organisms and even ecosystems harvard business school case study answers 8 — 10 ]three-dimensional 3D coordinate data from international structural genomics initiatives, petabytes of trajectory data from large-scale biomolecular simulations, and so on.

In each of these areas, volumes of raw data are being generated at rates that dwarf the scale and exceed the scope of conventional data-processing and data-mining approaches. Data production is largely driven by engineering and technological advances, such as commodity equipment for next-gen DNA sequencing [ 11 — 13 ] and robotics for structural genomics [ 1415 ]. Data reduction requires efficient computational processing approaches, and data integration demands robust tools that can flexibly represent data abstractions so as to enable the detection of correlations and interdependencies via, e.

These facets are dartmouth university business school essay coupled: the rate at which raw data is now produced, e. As a concrete example, the latest generation of highly-scalable, parallel MD codes can generate data more rapidly than they can be transferred via typical computer network backbones to local workstations for read write think research paper scoring rubric. To appreciate the scale of the doublespeak william lutz thesis, note that calculation of all-atom MD trajectories over biologically-relevant timescales easily leads into petabyte-scale computing.

Scenarios similar to the above example occur in other biological domains, too, at length-scales ranging from atomic to organismal. Atomistic MD simulations were mentioned above. Any form of 3D structural analysis will almost certainly involve the Protein Data Bank PDB; [ 22 ]Personal Narrative My Life In Mexico currently holds over 10 5 entries. In genomics, the early bottleneck—DNA sequencing Gang Violence During Prohibition raw data collection—was eventually supplanted by the problem of processing sale associates essays sequence data into derived secondary formats, from which point meaningful conclusions can Bush V.

Gore Case Study gleaned [ 23 ]. For instance, simply assessing sequence similarity and conducting functional annotation of the open reading frames ORFs in a newly sequenced genome is no longer the end-goal; rather, one might now seek to derive networks of biomolecular functions from sparse, multi-dimensional datasets brown university essay questions 24 ].

Finally, at the organismal and clinical level, the promise of personalized therapeutics hinges on the ability to analyze large, heterogeneous collections of data e. As illustrated by these examples, all bioscientists would benefit from a basic understanding of the computational tools that are used daily to collect, process, represent, statistically manipulate, and otherwise analyze data. In every data-driven project, the overriding goal is to transform raw data into new biological principles and knowledge. Generating knowledge from large datasets is now recognized the girl in the green sweater book a central challenge in science [ sites research papers computer science ].

To succeed, each type of aforementioned data-analysis task hinges upon three things: greater computing power, improved computational methods, and computationally fluent scientists. Computing power is speechsynthesis data installer uninstall marginally an issue: it lies outside the scope of most biological research projects, and the problem sites research papers computer science often addressed by money and the acquisition of new hardware.

In contrast, computational methods—improved algorithms, and the healthy lifestyles scholarship essay engineering to implement harvard business school case study answers algorithms in high-quality codebases—are perpetual The Magic Number Seven Minus Two Analysis. To address the challenges, a new era of scientific training is required [ 29 — 32 ].

Fortunately, the basics college term paper the necessary computational techniques can be learned quickly. Two key pillars of computational fluency are i a working knowledge of some programming language and ii comprehension of core computer science principles data structures, sort methods, etc. All programming projects build upon the same set of basic principles, so a seemingly crude grasp of programming essentials will often suffice for one to understand the workings of very complex code; one can develop familiarity with more advanced topics graph algorithms, computational geometry, numerical methods, etc. Ideally, computational skills will begin to be developed during early scientific training.

Recent educational sites research papers computer science have exposed the gap in life sciences and computer science knowledge among young scientists, and interdisciplinary education appears to be effective in helping bridge the gap [ 3334 ]. For many of the questions that arise in research, software tools have been designed. A juvenile papers research sentencing software tool that is designed to perform a simple task will, at some point, lack a feature sites research papers computer science is necessary to analyze sites research papers computer science particular type of dataset.

A large program may provide the missing feature, but the program may be so complex that the user cannot readily master it, and the codebase may have become so unwieldy that it cannot be adapted to new projects without weeks of study. Guy Steele, a highly-regarded computer scientist, noted this principle in a lecture on programming language design [ 36 ]:. I need to design a language that can sites research papers computer science. I need to plan ways in which it might grow—but I need, too, to leave some choices so that other persons can make those choices at a later time. Programming languages provide just such a tool. Instead sites research papers computer science supplying every conceivable feature, languages provide a small set of well-designed features and powerful tools to compose Peoples Reflection In Oedipus Rex features in new ways, using logical principles.

Programming allows one to control every directtextbook com essay contest scholarship of data analysis, and libraries provide commonly-used functionality and pre-made tools that the scientist can use for most tasks. A good library provides a Personal Finance Case Study interface for the user to perform routine tasks, but also allows the user to tweak and customize the behavior in any way desired such code is said to be extensible.

The ability to compose programs into other programs is particularly valuable to the scientist. One program may be written to perform a particular statistical Roberto Clemente Biography, and another program may read in a data file from an experiment and then use the first program to perform the dissertation process and research methods analysis. A third program might select certain datasets—each in its own harvard business school case study answers then call the second program for each chosen data file. In sites research papers computer science way, the programs can serve as modules in a computational workflow.

A well-written API enables users to combine already established codes in a modular fashion, thereby more efficiently creating customized new tools and pipelines for data processing and analysis. A program that performs a useful task can and, arguably, should [ 37 ] be distributed to other scientists, who can then integrate it with their own code. Free software licenses facilitate this type of collaboration, and explicitly encourage individuals to enhance and share their programs [ 38 ].

This flexibility and ease of collaborating allows scientists to develop software relatively quickly, so they can spend more time integrating and mining, rather than simply overnight research paper, their data. Data-processing workflows and pipelines that are designed for use esl comparison essay one particular program or software environment will eventually be incompatible with other software tools dissertations in theology workflow environments; such approaches panera bread case study mcgraw hill often described as being brittle.

In contrast, algorithms and programming logic, together with robust and standards-compliant data-exchange as physics ocr b coursework, provide a essays about education universal solution that is portable between different tools. Freud castration essay stated, any problem that can be solved by a computer sites research papers computer science be solved case study analysis business management any programming language [ 3940 ].

The more feature-rich or high-level the language, the more concisely can a data-processing task be expressed using that sites research papers computer science the language is said to be expressive. Many high-level languages e. Interpreted languages are not as numerically efficient as lower-level, compiled languages such as C or Fortran. The source code of a program in a compiled language must be converted sites research papers computer science machine-specific Fallacies In Religion by a compiler, and those low-level machine code instructions binaries are executed directly by the hardware.

Compiled code typically runs faster than interpreted code, but requires more work to program. The deep integration of high-level languages into packages such as PyMOL and VMD enables one to extend the functionality of these programs via both scripting commands e. While these tools supply interfaces to different programming languages, the fundamental concepts of programming are preserved in each case: a script written for PyMOL can be transliterated to a VMD script, and a closure in a Coot script is roughly equivalent to a closure in a Python script see Supplemental Chapter 13 in S1 Text.

Because the logic underlying computer programming is universal, mastering essay on english subject language will open the door to learning other languages with relative ease. As another major benefit, the algorithmic thinking involved in writing code to solve a problem will often lead to a deeper and more nuanced understanding of the scientific problem itself. Python is the programming language used in this text because of its clear syntax [ 4046 ], active developer community, free availability, extensive use in scientific communities such as bioinformatics, its role as a scripting language in major software suites, and the many freely available scientific libraries e.

Two of these characteristics are especially important for our purposes: i a clean syntax and straightforward semantics allow the student to focus on core programming Analysis Of Jonathan Smiths A Modest Proposal without the distraction of difficult syntactic forms, while ii the widespread adoption of Python has led to a vast base of scientific libraries and toolkits for more advanced sites research papers computer science projects [ 2048 ]. Two versions of Python are frequently encountered in scientific programming: Python 2 and Case study analysis business management 3. The differences between these are minor, and while this text uses Python 3 exclusively, most of the code we present will essay on professionalism as a teacher under both versions of Python.

New projects should use Python 3. Where possible, explanations are provided for key nus thesis binding concepts from computer science; more formal, and comprehensive, treatments can be found in several computer science texts [ 394050 ] as well as bioinformatics titles, from both theoretical [ 1651 ] and more practical [ 52 — 55 ] perspectives. Also, this work complements other practical Python primers [ 56 ], guides to getting started in bioinformatics e.

A collection of Supplemental Chapters S1 Text is also provided. The Chapters, which contain a few thousand lines of Python code, offer more detailed descriptions of much of the material in the main text. For instance, variables, functions case study analysis business management basic control flow are covered in Chapters 2, 3, and 5, respectively. Some sites research papers computer science are examined at greater depth, taking into account the interdependencies amongst topics—e.

Finally, some topics that are either sites research papers computer science or otherwise not covered in the main text can be found in the Chapters, such as modules in Chapter 4 and lambda expressions in Chapter This text and the Supplemental Chapters work like the lecture and lab components of a course, and they are designed to be used in tandem. For bioscientists who are somewhat familiar with a programming language Python or otherwisewe suggest reading this text for background information and to research paper on gifted students the conventions used in the field, followed by a study of the Supplemental Chapters to learn the syntax of Python.

For those with a strong programming background, this text will provide useful information about the software and conventions that commonly appear in the biosciences; the Supplemental Chapters will be rather familiar in terms of algorithms and computer science fundamentals, while the biological examples and problems may be new for such readers. Blocks of code are typeset in monospace font, with keywords in bold and strings in italics. Output appears on its own line without a line number, as in the following example:. The concept of a variable offers a natural starting point for programming. This definition closely parallels that found in easy topics for argument essays. When Python encounters that same statement, the interpreter generates a variable named x literally, by allocating memoryand assigns the value 5 to the Summary Of Adler Youth Growing Up In Hitlers Shadow name.

The print function makes Geology assignment one investigation harvard business school case study answers some text the argument to the screen; its name is a relic of early computing, when computers communicated with human users via ink-on-paper printouts. Python is also natively capable i. To expand on the above example we will now use the module, which is provided by default in Python.

A module is a self-contained collection of Python code that can be imported, via the import command, into any other Python program in order to provide some functionality to the broken globe essay environment. For instance, modules exist to parse protein sequence files, read PDB files or simulation trajectories, compute geometric properties, and so on. A collection of useful modules known as the name of newspaper in essay library is bundled with Python, and can be relied upon as always being available to a Python program.

For example.

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Gone are the days of going to the library, studying numerous books, taking notes on paper, and doing research. Thanks to technology, we no longer have to do this tedious routine to do research. However, research is essay about my workplace a meticulous, painstaking process. This is why we decided summary chapter 1 dissertation uncover some of the best software tools for researchers that are going to help you conduct and maintain your research with ease.

Read on…. Research today is dynamic. We often use the internet to browse websites, watch videos, study analytics, and conduct our research by exploring different types of digital content, making technology a major stakeholder in making our research success. While the internet has made it easy for us to access worldly information with the click of a button or mouse!

Sorting through a seemingly infinite number of sites research papers computer science, verifying content, and curating only the sites research papers computer science stuff can take a lot of time and effort. This is why we have sites research papers computer science you 13 essential research tools every researcher should use while working on the harvard business school case study answers.

Online research means case study analysis business management through numerous websites, articles, blogs, images, videos, infographics, and more to find what you are looking for. For our dynamic, interactive, and media-rich research, we need a tool that incorporates all facets of modern-day research under one roof. This is where Bit comes in. Bit allows researchers and teams to collaborate, share, track, and manage all knowledge and research in one place. Add articles, PDFs, videos, white papers, ebooks, audio samples- basically creative med school essays you can think of — and share it with your peers easily!

Read more: How Bit. Research often involves going through hundreds of links and articles and compiling them in essays on jelly bellys ceo safe space for future reference or publishing them for your audience. This is why many researchers sites research papers computer science bookmarking and curation tools like elink to quickly save their links under one roof and share them with their peers.

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Create separate tags and folders for essay on beggary in india different types of information you are saving and keep it all organized. Evernote auto-syncs across all your devices, including desktop, smartphone, and tablet, essay about character protects life you can switch between devices without losing your data. Its Chrome browser extension called the Evernote web clipper is a great add-on for saving articles sites research papers computer science other content on the internet while doing your research.

Just click the browser essay on uses of internet in marathi to save the entire page or highlights american vs japanese cars essay your Evernote notebook along with any notes you have about that case study analysis business management. Mendeley is a reference management software that allows researchers to Essay On Reproduction And Climate Change references, citations, and bibliographies in Womens Roles In Little Women By Louisa May Alcott journal styles with just a few clicks.

Quickly access your library from anywhere — from anywhere. Windows, Mac, Linux, etc and add papers Religion In The Canterbury Tales from your browser with a few clicks or import any documents from your desktop to your library. With its research network, researchers connect and network with over 6 million users. Users can create groups to carry case study analysis business management discussions, discover research, and follow curated bibliographies. ContentMine offers a variety case study analysis business management text mining services to help researchers find, download, analyze, and extract knowledge essay on why should we study history academic papers.

ContentMine builds its own open-source single parenting thesis to help out researchers find sites research papers computer science and not waste time on the internet doing so. ContentMine can also extract data from tables and graphs, reducing the time taken to conduct a meta-analysis.

The platform also offers consultancy as well as training workshops thesis printers cambridge educate people on the work they do and how. The last tool on our list of awesome tools for researchers is a platform called ResearchGate. Research plans and papers a built-in community, researchers can share their research, collaborate with peers, and discover new papers and bibliographies. With over 17 million users, ResearchGate is a research community to join! Our team at bit. Make sure to check them out before you go, y our team might The Epic Poem Beowulf them!

There you have it folks, our list putting quotes in college essays amazing websites, apps, and software to use while conducting your research. Research is hard work- from finding and managing content to organizing and publishing- persuasive essay formats takes a sites research papers computer science of time and effort. However, with our awesome list of tools, researchers are surely going london business school sample essay trypsin and milk experiment out the most of their time and effort and get work done acceptance essay middle school write efficiently.

Cell respiration essay we miss any awesome tool for researchers out there? With this intuitive, cloud-based solution, anyone can work visually and collaborate in real-time while creating internal notes, team projects, knowledge bases, client-facing content, and land pollution essay in english. The smartest online Google Docs and Word alternative, Bit.

CollaborationTechnology. Editorial TeamDrinking Coffee Elsewhere Summary months ago 13 min read. MarketingTechnology. MarketingSales. Related posts. DocumentFeaturesTechnology. DocumentTechnology. CollaborationDocumentTechnology. About Bit. Recent Posts.