Workflow And Pipeline Of Hybrid Genome Assembly
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A workflow consists of an orchestrated and repeatable pattern of activity, enabled by the
system A system is a group of Interaction, interacting or interrelated elements that act according to a set of rules to form a unified whole. A system, surrounded and influenced by its environment (systems), environment, is described by its boundaries, ...
atic organization of
resource Resource refers to all the materials available in our environment which are technologically accessible, economically feasible and culturally sustainable and help us to satisfy our needs and wants. Resources can broadly be classified upon their ...
s into
process A process is a series or set of activities that interact to produce a result; it may occur once-only or be recurrent or periodic. Things called a process include: Business and management *Business process, activities that produce a specific se ...
es that transform materials, provide services, or process information. It can be depicted as a sequence of operations, the work of a person or group, the work of an organization of staff, or one or more simple or complex mechanisms. From a more abstract or higher-level perspective, workflow may be considered a view or representation of real work. The flow being described may refer to a
document A document is a written, drawn, presented, or memorialized representation of thought, often the manifestation of non-fictional, as well as fictional, content. The word originates from the Latin ''Documentum'', which denotes a "teaching" or ...
, service, or product that is being transferred from one step to another. Workflows may be viewed as one fundamental building block to be combined with other parts of an organization's structure such as information technology,
team A team is a group of individuals (human or non-human) working together to achieve their goal. As defined by Professor Leigh Thompson (academic), Leigh Thompson of the Kellogg School of Management, " team is a group of people who are interde ...
s,
project A project is any undertaking, carried out individually or collaboratively and possibly involving research or design, that is carefully planned to achieve a particular goal. An alternative view sees a project managerially as a sequence of even ...
s and hierarchies.


Historical development

The development of the concept of a workflow occurred above a series of loosely defined, overlapping eras.


Beginnings in manufacturing

The modern history of workflows can be traced to Frederick Taylor and Henry Gantt, although the term "workflow" was not in use as such during their lifetimes. One of the earliest instances of the term "work flow" was in a railway engineering journal from 1921. Taylor and Gantt launched the study of the deliberate, rational organization of work, primarily in the context of manufacturing. This gave rise to
time and motion studies A time and motion study (or time-motion study) is a business efficiency technique combining the Time Study work of Frederick Winslow Taylor with the Motion Study work of Frank and Lillian Gilbreth (the same couple as is best known through the biog ...
. Related concepts include
job shop Job shops are typically small manufacturing systems that handle job production, that is, custom/bespoke or semi-custom/bespoke manufacturing processes such as small to medium-size customer orders or batch jobs. Job shops typically move on to diffe ...
s and
queuing systems Queueing theory is the mathematical study of waiting lines, or queues. A queueing model is constructed so that queue lengths and waiting time can be predicted. Queueing theory is generally considered a branch of operations research because the ...
(
Markov chain A Markov chain or Markov process is a stochastic model describing a sequence of possible events in which the probability of each event depends only on the state attained in the previous event. Informally, this may be thought of as, "What happe ...
s). The 1948 book ''
Cheaper by the Dozen ''Cheaper by the Dozen'' is a semi-autobiographical novel written by Frank Bunker Gilbreth Jr. and Ernestine Gilbreth Carey, published in 1948. The novel recounts the authors' childhood lives growing up in a household of 12 children. The bestsell ...
'' introduced the emerging concepts to the context of family life.


Maturation and growth

The invention of the
typewriter A typewriter is a mechanical or electromechanical machine for typing characters. Typically, a typewriter has an array of keys, and each one causes a different single character to be produced on paper by striking an inked ribbon selectivel ...
and the copier helped spread the study of the rational organization of labor from the manufacturing shop floor to the office. Filing systems and other sophisticated systems for managing physical
information Information is an abstract concept that refers to that which has the power to inform. At the most fundamental level information pertains to the interpretation of that which may be sensed. Any natural process that is not completely random ...
flows evolved. Several events likely contributed to the development of formalized information workflows. First, the field of optimization theory matured and developed
mathematical optimization Mathematical optimization (alternatively spelled ''optimisation'') or mathematical programming is the selection of a best element, with regard to some criterion, from some set of available alternatives. It is generally divided into two subfi ...
techniques. For example, Soviet mathematician and economist
Leonid Kantorovich Leonid Vitalyevich Kantorovich ( rus, Леони́д Вита́льевич Канторо́вич, , p=lʲɪɐˈnʲit vʲɪˈtalʲjɪvʲɪtɕ kəntɐˈrovʲɪtɕ, a=Ru-Leonid_Vitaliyevich_Kantorovich.ogg; 19 January 19127 April 1986) was a Soviet ...
developed the seeds of
linear programming Linear programming (LP), also called linear optimization, is a method to achieve the best outcome (such as maximum profit or lowest cost) in a mathematical model whose requirements are represented by linear function#As a polynomial function, li ...
in 1939 through efforts to solve a plywood manufacturer's production optimization issues. Second,
World War II World War II or the Second World War, often abbreviated as WWII or WW2, was a world war that lasted from 1939 to 1945. It involved the vast majority of the world's countries—including all of the great powers—forming two opposin ...
and the Apollo program drove process improvement forward with their demands for the rational organization of work.


Quality era

In the post-war era, the work of
W. Edwards Deming William Edwards Deming (October 14, 1900 – December 20, 1993) was an American engineer, statistician, professor, author, lecturer, and management consultant. Educated initially as an electrical engineer and later specializing in mathematical ...
and
Joseph M. Juran Joseph Moses Juran (December 24, 1904 – February 28, 2008) was a Romanian-born American engineer and management consultant. He was an evangelist for quality and quality management, having written several books on those subjects. He was the brot ...
led to a focus on quality, first in Japanese companies, and more globally from the 1980s: there were various movements ranging from total quality management to Six Sigma, and then more qualitative notions of business process re-engineering. This led to more efforts to improve workflows, in
knowledge economy The knowledge economy (or the knowledge-based economy) is an economic system in which the production of goods and services is based principally on knowledge-intensive activities that contribute to advancement in technical and scientific inno ...
sectors as well as in manufacturing. Variable demands on workflows were recognised when the theory of critical paths and moving bottlenecks was considered.


Worflow management

Basu and Kumar note that the term "workflow management" has been used to refer to tasks associated with the flow of information through the
value chain A value chain is a progression of activities that a firm operating in a specific industry performs in order to deliver a valuable product (i.e., good and/or service) to the end customer. The concept comes through business management and was firs ...
rather than the flow of material goods: they characterise the definition, analysis and management of information as "workflow management". They note that workflow can be managed within a single organisation, where distinct roles are allocated to individual resources, and also across multiple organisations or distributed locations, where attention needs to be paid to the interactions between activities which are located at the organizational or locational boundaries. The transmission of information from one organization to another is a critical issue in this inter-organizational context and raises the importance of tasks they describe as "validation", "verification" and "data usage analysis".


Workflow management systems

A workflow management system (WfMS) is a software system for setting up, performing, and monitoring a defined sequence of processes and tasks, with the broad goals of increasing productivity, reducing costs, becoming more agile, and improving information exchange within an organization. These systems may be process-centric or data-centric, and they may represent the workflow as graphical maps. A workflow management system may also include an extensible interface so that external software applications can be integrated and provide support for wide area workflows that provide faster response times and improved productivity.


Related concepts

The concept of workflow is closely related to several fields in
operations research Operations research ( en-GB, operational research) (U.S. Air Force Specialty Code: Operations Analysis), often shortened to the initialism OR, is a discipline that deals with the development and application of analytical methods to improve deci ...
and other areas that study the nature of work, either quantitatively or qualitatively, such as
artificial intelligence Artificial intelligence (AI) is intelligence—perceiving, synthesizing, and inferring information—demonstrated by machines, as opposed to intelligence displayed by animals and humans. Example tasks in which this is done include speech re ...
(in particular, the sub-discipline of AI planning) and
ethnography Ethnography (from Greek ''ethnos'' "folk, people, nation" and ''grapho'' "I write") is a branch of anthropology and the systematic study of individual cultures. Ethnography explores cultural phenomena from the point of view of the subject o ...
. The term "workflow" is more commonly used in particular industries, such as in printing or professional domains such as clinical laboratories, where it may have particular specialized meanings. # Processes: A process is a more general notion than workflow and can apply to, for example, physical or biological processes, whereas a workflow is typically a process or collection of processes described in the context of work, such as all processes occurring in a machine shop. # Planning and scheduling: A plan is a description of the logically necessary, partially ordered set of activities required to accomplish a specific goal given certain starting conditions. A plan, when augmented with a schedule and
resource allocation In economics, resource allocation is the assignment of available resources to various uses. In the context of an entire economy, resources can be allocated by various means, such as markets, or planning. In project management, resource allocation ...
calculations, completely defines a particular ''instance'' of systematic processing in pursuit of a goal. A workflow may be viewed as an often optimal or near-optimal realization of the mechanisms required to execute the same plan repeatedly. # Flow control: This is a control concept applied to workflows, to distinguish from static control of buffers of material or orders, to mean a more dynamic control of flow speed and flow volumes in motion and in process. Such orientation to dynamic aspects is the basic foundation to prepare for more advanced job shop controls, such as just-in-time or just-in-sequence. # In-transit visibility: This monitoring concept applies to transported material as well as to work in process or work in progress, i.e., workflows.


Examples

The following examples illustrate the variety of workflows seen in various contexts: # In machine shops, particularly
job shop Job shops are typically small manufacturing systems that handle job production, that is, custom/bespoke or semi-custom/bespoke manufacturing processes such as small to medium-size customer orders or batch jobs. Job shops typically move on to diffe ...
s and flow shops, the flow of a part through the various processing stations is a workflow. # Insurance claims processing is an example of an information-intensive, document-driven workflow. # Wikipedia editing can be modeled as a stochastic workflow. # The
Getting Things Done ''Getting Things Done'' (GTD) is a personal productivity system developed by David Allen and published in a book of the same name. GTD is described as a time management system. Allen states "there is an inverse relationship between things on yo ...
system is a model of personal workflow management for information workers. # In software development, support and other industries, the concept of ''
follow-the-sun Follow the Sun (FTS), a sub-field of globally distributed software engineering (GDSE), is a type of global knowledge workflow designed in order to reduce the time to market, in which the knowledge product is owned and advanced by a production si ...
'' describes a process of passing unfinished work across time zones. # In traditional offset and digital printing, the concept of workflow represents the process, people, and usually software technology (RIPs raster image processors or DFE digital front end) controllers that play a part in pre/post processing of print-related files, e.g., PDF pre-flight checking to make certain that fonts are embedded or that the imaging output to plate or digital press will be able to render the document intent properly for the image-output capabilities of the press that will print the final image. # In scientific experiments, the overall process (tasks and data flow) can be described as a
directed acyclic graph In mathematics, particularly graph theory, and computer science, a directed acyclic graph (DAG) is a directed graph with no directed cycles. That is, it consists of vertices and edges (also called ''arcs''), with each edge directed from one ve ...
(DAG). This DAG is referred to as a workflow, e.g., Brain Imaging workflows. # In healthcare data analysis, a workflow can be identified or used to represent a sequence of steps which compose a complex data analysis. # In
service-oriented architecture In software engineering, service-oriented architecture (SOA) is an architectural style that focuses on discrete services instead of a monolithic design. By consequence, it is also applied in the field of software design where services are provide ...
s, an application can be represented through an executable workflow, where different, possibly geographically distributed, service components interact to provide the corresponding functionality under the control of a workflow management system. # In
shared services Shared services is the provision of a service by one part of an organization or group, where that service had previously been found, in more than one part of the organization or group. Thus the funding and resourcing of the service is shared and th ...
, an application can be in the practice of developing robotic process automation (called RPA or RPAAI for self-guided RPA 2.0 based on artificial intelligence) which results in the deployment of attended or unattended software agents to an organization's environment. These software agents, or robots, are deployed to perform pre-defined structured and repetitive sets of business tasks or processes. Artificial intelligence software robots are deployed to handle unstructured data sets and are deployed after performing and deploying robotic process automation.


Features and phenomenology

# Modeling: Workflow problems can be modeled and analyzed using graph-based formalisms like Petri nets. # Measurement: Many of the concepts used to measure scheduling systems in
operations research Operations research ( en-GB, operational research) (U.S. Air Force Specialty Code: Operations Analysis), often shortened to the initialism OR, is a discipline that deals with the development and application of analytical methods to improve deci ...
are useful for measuring general workflows. These include throughput, processing time, and other regular metrics. # Specialized connotations: The term "workflow" has specialized connotations in information technology, document management, and imaging. Since 1993, one trade consortium specifically focused on workflow management and the interoperability of workflow management systems, the
Workflow Management Coalition Workflow Management Coalition (WfMC) was a consortium formed to define standardization, standards for the interoperability of workflow management systems. The coalition was disbanded in 2019 and no longer exists. History The Coalition was found ...
. #
Scientific workflow system A scientific workflow system is a specialized form of a workflow management system designed specifically to compose and execute a series of computational or data manipulation steps, or workflow, in a scientific application. Applications Distribute ...
s: These found wide acceptance in the fields of
bioinformatics Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combi ...
and
cheminformatics Cheminformatics (also known as chemoinformatics) refers to use of physical chemistry theory with computer and information science techniques—so called "''in silico''" techniques—in application to a range of descriptive and prescriptive problem ...
in the early 2000s, when they met the need for multiple interconnected tools that handle multiple data formats and large data quantities. Also, the paradigm of scientific workflows resembles the well-established practice of
Perl Perl is a family of two high-level, general-purpose, interpreted, dynamic programming languages. "Perl" refers to Perl 5, but from 2000 to 2019 it also referred to its redesigned "sister language", Perl 6, before the latter's name was offici ...
programming in life science research organizations, making this adoption a natural step towards more structured infrastructure setup. # Human-machine interaction: Several conceptualizations of mixed-initiative workflows have been studied, particularly in the military, where automated agents play roles just as humans do. For innovative, adaptive, and collaborative human work, the techniques of human interaction management are required. # Workflow analysis: Workflow systems allow users to develop executable processes with no familiarity with formal programming concepts. Automated workflow analysis techniques can help users analyze the properties of user workflows to conduct verification of certain properties before executing them, e.g., analyzing flow control or data flow. Examples of tools based on formal analysis frameworks have been developed and used for the analysis of scientific workflows and can be extended to the analysis of other types of workflows.


Workflow improvement theories

Several workflow improvement theories have been proposed and implemented in the modern workplace. These include: # Six Sigma # Total Quality Management #
Business Process Reengineering Business process re-engineering (BPR) is a business management strategy originally pioneered in the early 1990s, focusing on the analysis and design of workflows and business processes within an organization. BPR aims to help organizations fundam ...
#
Lean Lean, leaning or LEAN may refer to: Business practices * Lean thinking, a business methodology adopted in various fields ** Lean construction, an adaption of lean manufacturing principles to the design and construction process ** Lean governmen ...
systems # Theory of Constraints Evaluation of resources, both physical and human, is essential to evaluate hand-off points and potential to create smoother transitions between tasks.


Components

A workflow can usually be described using formal or informal flow diagramming techniques, showing directed flows between processing steps. Single processing steps or components of a workflow can basically be defined by three parameters: #input description: the information, material and energy required to complete the step #transformation rules:
algorithm In mathematics and computer science, an algorithm () is a finite sequence of rigorous instructions, typically used to solve a class of specific Computational problem, problems or to perform a computation. Algorithms are used as specificat ...
s which may be carried out by people or machines, or both #output description: the information, material, and energy produced by the step and provided as input to downstream steps Components can only be plugged together if the output of one previous (set of) component(s) is equal to the mandatory input requirements of the following component(s). Thus, the essential description of a component actually comprises only input and output that are described fully in terms of
data type In computer science and computer programming, a data type (or simply type) is a set of possible values and a set of allowed operations on it. A data type tells the compiler or interpreter how the programmer intends to use the data. Most progra ...
s and their meaning (
semantics Semantics (from grc, σημαντικός ''sēmantikós'', "significant") is the study of reference, meaning, or truth. The term can be used to refer to subfields of several distinct disciplines, including philosophy Philosophy (f ...
). The algorithms' or rules' descriptions need only be included when there are several alternative ways to transform one type of input into one type of output – possibly with different accuracy, speed, etc. When the components are non-local services that are invoked remotely via a computer network, such as Web services, additional descriptors (such as QoS and availability) also must be considered.


Applications

Many software systems exist to support workflows in particular domains. Such systems manage tasks such as automatic routing, partially automated processing, and integration between different functional software applications and hardware systems that contribute to the value-addition process underlying the workflow. There are also software suppliers using the technology process driven messaging service based upon three elements: * Standard Objects * Workflow Objects * Workflow


See also

*
Bioinformatics workflow management systems A bioinformatics workflow management system is a specialized form of workflow management system designed specifically to compose and execute a series of computational or data manipulation steps, or a workflow, that relate to bioinformatics. Ther ...
*
Business process automation Business process automation (BPA), also known as business automation or digital transformation, is the technology-enabled automation of complex business processes. It can streamline a business for simplicity, achieve digital transformation, increa ...
* Business process management * Business process modeling * Computer-supported collaboration * DRAKON visual language for business process modeling *
Enterprise content management Enterprise content management (ECM) extends the concept of content management by adding a timeline for each content item and, possibly, enforcing processes for its creation, approval and distribution. Systems using ECM generally provide a secure ...
* Process architecture *
Process-driven application A process-driven application is a software application that is driven by an underlying process or workflow engine where the process can be exposed and reused. In effect all applications are process-driven and the logic of any application can be extr ...
*
Workflow engine A workflow engine is a software application that manages business processes. It is a key component in workflow technology and typically makes use of a database server. A workflow engine manages and monitors the state of activities in a workflow, su ...
*
Workforce modeling {{peacock, date=January 2014 Workforce modeling is the process by which the need for skilled workers at a particular point in time (demand) is matched directly with the availability and preference of skilled workers (supply). The resulting mathemat ...
*
Business process reengineering Business process re-engineering (BPR) is a business management strategy originally pioneered in the early 1990s, focusing on the analysis and design of workflows and business processes within an organization. BPR aims to help organizations fundam ...


References


Further reading

* Ryan K. L. Ko, Stephen S. G. Lee, Eng Wah Lee (2009) Business Process Management (BPM) Standards: A Survey. In: Business Process Management Journal, Emerald Group Publishing Limited. Volume 15 Issue 5.
PDF
* Khalid Belhajjame, Christine Collet, Genoveva Vargas-Solar
A Flexible Workflow Model for Process-Oriented Applications
WISE (1) 2001, IEEE CS, 2001. *Layna Fischer (ed.): 2007 BPM and Workflow Handbook, Future Strategies Inc., *Layna Fischer: ''Workflow Handbook 2005'', Future Strategies, *Layna Fischer: ''Excellence in Practice, Volume V: Innovation and Excellence in Workflow and Business Process Management'', *Thomas L. Friedman: ''The World Is Flat: A Brief History of the Twenty-first Century'', Farrar, Straus and Giroux, *Keith Harrison-Broninski. ''Human Interactions: The Heart and Soul of Business Process Management''. *Holly Yu: ''Content and Work Flow Management for Library Websites: Case Studies'', Information Science Publishing, *
Wil van der Aalst Willibrordus Martinus Pancratius van der Aalst (born 29 January 1966) is a Dutch computer scientist and full professor at RWTH Aachen University, leading the Process and Data Science (PADS) group. His research and teaching interests include i ...
, Kees van Hee: ''Workflow Management: Models, Methods, and Systems'', B&T, *Setrag Khoshafian, Marek Buckiewicz: ''Introduction to Groupware, Workflow and Workgroup Computing'', John Wiley & Sons, *Rashid N. Kahn: ''Understanding Workflow Automation: A Guide to Enhancing Customer Loyalty'', Prentice Hall, *Dan C. Marinescu: ''Internet-Based Workflow Management: Towards a Semantic Web'', John Wiley & Sons, *Frank Leymann, Dieter Roller: ''Production Workflow: Concepts and Techniques'', Prentice Hall, * Michael Jackson, Graham Twaddle: ''Business Process Implementation: Building Workflow Systems'', Addison-Wesley, *Alec Sharp, Patrick McDermott: ''Workflow Modeling'', Artech House Publishers, *Toni Hupp: ''Designing Work Groups, Jobs, and Work Flow'', Pfeiffer & Company, *Gary Poyssick, Steve Hannaford: ''Workflow Reengineering'', Adobe, *Dave Chaffey: ''Groupware, Workflow and Intranets: Reengineering the Enterprise with Collaborative Software'', Digital Press, *Wolfgang Gruber: ''Modeling and Transformation of Workflows With Temporal Constraints'', IOS Press, *Andrzej Cichocki, Marek Rusinkiewicz, Darrell Woelk: ''Workflow and Process Automation Concepts and Technology'', Kluwer Academic Publishers, *Alan R. Simon, William Marion: ''Workgroup Computing: Workflow, Groupware, and Messaging'', McGraw-Hill, *Penny Ann Dolin: ''Exploring Digital Workflow'', Delmar Thomson Learning, *Gary Poyssick: ''Managing Digital Workflow'', Prentice Hall, *Frank J. Romano: ''PDF Printing & Workflow'', Prentice Hall, *James G. Kobielus: ''Workflow Strategies'', Hungry Minds, *Alan Rickayzen, Jocelyn Dart, Carsten Brennecke: ''Practical Workflow for SAP'', Galileo, *Alan Pelz-Sharpe, Angela Ashenden: ''E-process: Workflow for the E-business'', Ovum, *Stanislaw Wrycza: ''Systems Development Methods for Databases, Enterprise Modeling, and Workflow Management'', Kluwer Academic/Plenum Publishers, *''Database Support for Workflow Management'', Kluwer Academic Publishers, *Matthew Searle: ''Developing With Oracle Workflow'' * V. Curcin and M. Ghanem
Scientific workflow systems - can one size fit all?
paper in CIBEC'08 comparing scientific workflow systems.


External links


Workflow PatternsWorkflow Management Coalition
{{Authority control Groupware Business process