Microarray analysis techniques

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Microarray_analysis_techniques 

 

Example of an approximately 40,000 probe spotted oligo microarray with enlarged inset to show detail.

 

Microarray analysis techniques are used in interpreting the data generated from experiments on DNA (Gene chip analysis), RNA, and protein microarrays, which allow researchers to investigate the expression state of a large number of genes - in many cases, an organism's entire genome - in a single experiment. Such experiments can generate very large amounts of data, allowing researchers to assess the overall state of a cell or organism. Data in such large quantities is difficult - if not impossible - to analyze without the help of computer programs.

Introduction

Microarray data analysis is the final step in reading and processing data produced by a microarray chip. Samples undergo various processes including purification and scanning using the microchip, which then produces a large amount of data that requires processing via computer software. It involves several distinct steps, as outlined in the image below. Changing any one of the steps will change the outcome of the analysis, so the MAQC Project was created to identify a set of standard strategies. Companies exist that use the MAQC protocols to perform a complete analysis.

The steps required in a microarray experiment

Techniques

National Center for Toxicological Research scientist reviews microarray data

 

Most microarray manufacturers, such as Affymetrix and Agilent, provide commercial data analysis software alongside their microarray products. There are also open source options that utilize a variety of methods for analyzing microarray data.

Aggregation and normalization

Comparing two different arrays or two different samples hybridized to the same array generally involves making adjustments for systematic errors introduced by differences in procedures and dye intensity effects. Dye normalization for two color arrays is often achieved by local regression. LIMMA provides a set of tools for background correction and scaling, as well as an option to average on-slide duplicate spots. A common method for evaluating how well normalized an array is, is to plot an MA plot of the data. MA plots can be produced using programs and languages such as R, MATLAB, and Excel. 

Raw Affy data contains about twenty probes for the same RNA target. Half of these are "mismatch spots", which do not precisely match the target sequence. These can theoretically measure the amount of nonspecific binding for a given target. Robust Multi-array Average (RMA) is a normalization approach that does not take advantage of these mismatch spots, but still must summarize the perfect matches through median polish. The median polish algorithm, although robust, behaves differently depending on the number of samples analyzed. Quantile normalization, also part of RMA, is one sensible approach to normalize a batch of arrays in order to make further comparisons meaningful.

The current Affymetrix MAS5 algorithm, which uses both perfect match and mismatch probes, continues to enjoy popularity and do well in head to head tests.

Flowchart showing how the MAS5 algorithm by Agilent works.

 

Factor Analysis for Robust Microarray Summarization (FARMS) is a model-based technique for summarizing array data at perfect match probe level. It is based on a factor analysis model for which a Bayesian maximum a posteriori method optimizes the model parameters under the assumption of Gaussian measurement noise. According to the Affycomp benchmark FARMS outperformed all other summarizations methods with respect to sensitivity and specificity.

Identification of significant differential expression

Many strategies exist to identify array probes that show an unusual level of over-expression or under-expression. The simplest one is to call "significant" any probe that differs by an average of at least twofold between treatment groups. More sophisticated approaches are often related to t-tests or other mechanisms that take both effect size and variability into account. Curiously, the p-values associated with particular genes do not reproduce well between replicate experiments, and lists generated by straight fold change perform much better. This represents an extremely important observation, since the point of performing experiments has to do with predicting general behavior. The MAQC group recommends using a fold change assessment plus a non-stringent p-value cutoff, further pointing out that changes in the background correction and scaling process have only a minimal impact on the rank order of fold change differences, but a substantial impact on p-values.

Clustering

Clustering is a data mining technique used to group genes having similar expression patterns. Hierarchical clustering, and k-means clustering are widely used techniques in microarray analysis.

Hierarchical clustering

Hierarchical clustering is a statistical method for finding relatively homogeneous clusters. Hierarchical clustering consists of two separate phases. Initially, a distance matrix containing all the pairwise distances between the genes is calculated. Pearson’s correlation and Spearman’s correlation are often used as dissimilarity estimates, but other methods, like Manhattan distance or Euclidean distance, can also be applied. Given the number of distance measures available and their influence in the clustering algorithm results, several studies have compared and evaluated different distance measures for the clustering of microarray data, considering their intrinsic properties and robustness to noise. After calculation of the initial distance matrix, the hierarchical clustering algorithm either (A) joins iteratively the two closest clusters starting from single data points (agglomerative, bottom-up approach, which is fairly more commonly used), or (B) partitions clusters iteratively starting from the complete set (divisive, top-down approach). After each step, a new distance matrix between the newly formed clusters and the other clusters is recalculated. Hierarchical cluster analysis methods include:

• Single linkage (minimum method, nearest neighbor)
• Average linkage (UPGMA).
• Complete linkage (maximum method, furthest neighbor)

Different studies have already shown empirically that the Single linkage clustering algorithm produces poor results when employed to gene expression microarray data and thus should be avoided.

K-means clustering

K-means clustering is an algorithm for grouping genes or samples based on pattern into K groups. Grouping is done by minimizing the sum of the squares of distances between the data and the corresponding cluster centroid. Thus the purpose of K-means clustering is to classify data based on similar expression. K-means clustering algorithm and some of its variants (including k-medoids) have been shown to produce good results for gene expression data (at least better than hierarchical clustering methods). Empirical comparisons of k-means, k-medoids, hierarchical methods and, different distance measures can be found in the literature.

Pattern recognition

Commercial systems for gene network analysis such as Ingenuity and Pathway studio create visual representations of differentially expressed genes based on current scientific literature. Non-commercial tools such as FunRich, GenMAPP and Moksiskaan also aid in organizing and visualizing gene network data procured from one or several microarray experiments. A wide variety of microarray analysis tools are available through Bioconductor written in the R programming language. The frequently cited SAM module and other microarray tools are available through Stanford University. Another set is available from Harvard and MIT.

Example of FunRich tool output. Image shows the result of comparing 4 different genes.

 

Specialized software tools for statistical analysis to determine the extent of over- or under-expression of a gene in a microarray experiment relative to a reference state have also been developed to aid in identifying genes or gene sets associated with particular phenotypes. One such method of analysis, known as Gene Set Enrichment Analysis (GSEA), uses a Kolmogorov-Smirnov-style statistic to identify groups of genes that are regulated together. This third-party statistics package offers the user information on the genes or gene sets of interest, including links to entries in databases such as NCBI's GenBank and curated databases such as Biocarta and Gene Ontology. Protein complex enrichment analysis tool (COMPLEAT) provides similar enrichment analysis at the level of protein complexes. The tool can identify the dynamic protein complex regulation under different condition or time points. Related system, PAINT and SCOPE performs a statistical analysis on gene promoter regions, identifying over and under representation of previously identified transcription factor response elements. Another statistical analysis tool is Rank Sum Statistics for Gene Set Collections (RssGsc), which uses rank sum probability distribution functions to find gene sets that explain experimental data. A further approach is contextual meta-analysis, i.e. finding out how a gene cluster responds to a variety of experimental contexts. Genevestigator is a public tool to perform contextual meta-analysis across contexts such as anatomical parts, stages of development, and response to diseases, chemicals, stresses, and neoplasms.

Significance analysis of microarrays (SAM)

Significance analysis of microarrays (SAM) is a statistical technique, established in 2001 by Virginia Tusher, Robert Tibshirani and Gilbert Chu, for determining whether changes in gene expression are statistically significant. With the advent of DNA microarrays, it is now possible to measure the expression of thousands of genes in a single hybridization experiment. The data generated is considerable, and a method for sorting out what is significant and what isn't is essential. SAM is distributed by Stanford University in an R-package. 

SAM identifies statistically significant genes by carrying out gene specific t-tests and computes a statistic d_j for each gene j, which measures the strength of the relationship between gene expression and a response variable. This analysis uses non-parametric statistics, since the data may not follow a normal distribution. The response variable describes and groups the data based on experimental conditions. In this method, repeated permutations of the data are used to determine if the expression of any gene is significant related to the response. The use of permutation-based analysis accounts for correlations in genes and avoids parametric assumptions about the distribution of individual genes. This is an advantage over other techniques (e.g., ANOVA and Bonferroni), which assume equal variance and/or independence of genes.

Basic protocol

• Perform microarray experiments — DNA microarray with oligo and cDNA primers, SNP arrays, protein arrays, etc.
• Input Expression Analysis in Microsoft Excel — see below
• Run SAM as a Microsoft Excel Add-Ins
• Adjust the Delta tuning parameter to get a significant # of genes along with an acceptable false discovery rate (FDR)) and Assess Sample Size by calculating the mean difference in expression in the SAM Plot Controller
• List Differentially Expressed Genes (Positively and Negatively Expressed Genes)

Running SAM

• SAM is available for download online at http://www-stat.stanford.edu/~tibs/SAM/ for academic and non-academic users after completion of a registration step.
• SAM is run as an Excel Add-In, and the SAM Plot Controller allows Customization of the False Discovery Rate and Delta, while the SAM Plot and SAM Output functionality generate a List of Significant Genes, Delta Table, and Assessment of Sample Sizes
• Permutations are calculated based on the number of samples
• Block Permutations
  • Blocks are batches of microarrays; for example for eight samples split into two groups (control and affected) there are 4!=24 permutations for each block and the total number of permutations is (24)(24)= 576. A minimum of 1000 permutations are recommended;

the number of permutations is set by the user when imputing correct values for the data set to run SAM

Response formats

Types:

• Quantitative — real-valued (such as heart rate)
• One class — tests whether the mean gene expression differs from zero
• Two class — two sets of measurements
  • Unpaired — measurement units are different in the two groups; e.g. control and treatment groups with samples from different patients
  • Paired — same experimental units are measured in the two groups; e.g. samples before and after treatment from the same patients
• Multiclass — more than two groups with each containing different experimental units; generalization of two class unpaired type
• Survival — data of a time until an event (for example death or relapse)
• Time course — each experimental units is measured at more than one time point; experimental units fall into a one or two class design
• Pattern discovery — no explicit response parameter is specified; the user specifies eigengene (principal component) of the expression data and treats it as a quantitative response

Algorithm

SAM calculates a test statistic for relative difference in gene expression based on permutation analysis of expression data and calculates a false discovery rate. The principal calculations of the program are illustrated below.

The s_o constant is chosen to minimize the coefficient of variation of d_i. r_i is equal to the expression levels (x) for gene i under y experimental conditions.

${\displaystyle \mathrm {False\ discovery\ rate\ (FDR)={\frac {Median\ (or\ 90^{th}\ percentile)\ of\ \#\ of\ falsely\ called\ genes}{Number\ of\ genes\ called\ significant}}} }$

Fold changes (t) are specified to guarantee genes called significant change at least a pre-specified amount. This means that the absolute value of the average expression levels of a gene under each of two conditions must be greater than the fold change (t) to be called positive and less than the inverse of the fold change (t) to be called negative. 

The SAM algorithm can be stated as:

1. Order test statistics according to magnitude 
2. For each permutation compute the ordered null (unaffected) scores
3. Plot the ordered test statistic against the expected null scores
4. Call each gene significant if the absolute value of the test statistic for that gene minus the mean test statistic for that gene is greater than a stated threshold 
5. Estimate the false discovery rate based on expected versus observed values 

Output

• Significant gene sets
  • Positive gene set — higher expression of most genes in the gene set correlates with higher values of the phenotype y
  • Negative gene set — lower expression of most genes in the gene set correlates with higher values of the phenotype y

SAM features

• Data from Oligo or cDNA arrays, SNP array, protein arrays,etc. can be utilized in SAM
• Correlates expression data to clinical parameters
• Correlates expression data with time
• Uses data permutation to estimates False Discovery Rate for multiple testing
• Reports local false discovery rate (the FDR for genes having a similar d_i as that gene) and miss rates
• Can work with blocked design for when treatments are applied within different batches of arrays
• Can adjust threshold determining number of gene called significant

Error correction and quality control

Quality control

Entire arrays may have obvious flaws detectable by visual inspection, pairwise comparisons to arrays in the same experimental group, or by analysis of RNA degradation. Results may improve by removing these arrays from the analysis entirely.

Background correction

Depending on the type of array, signal related to nonspecific binding of the fluorophore can be subtracted to achieve better results. One approach involves subtracting the average signal intensity of the area between spots. A variety of tools for background correction and further analysis are available from TIGR, Agilent (GeneSpring), and Ocimum Bio Solutions (Genowiz).

Spot filtering

Visual identification of local artifacts, such as printing or washing defects, may likewise suggest the removal of individual spots. This can take a substantial amount of time depending on the quality of array manufacture. In addition, some procedures call for the elimination of all spots with an expression value below a certain intensity threshold.

Landscape urbanism

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Landscape_urbanism 

Landscape urbanism is a theory of urban design arguing that the city is constructed of interconnected and ecologically rich horizontal field conditions, rather than the arrangement of objects and buildings. Landscape Urbanism, like Infrastructural Urbanism and Ecological Urbanism, emphasizes performance over pure aesthetics and utilizes systems-based thinking and design strategies. The phrase 'landscape urbanism' first appeared in the mid 1990s. Since this time, the phrase 'landscape urbanism' has taken on many different uses, but is most often cited as a postmodernist or post-postmodernist response to the "failings" of New Urbanism and the shift away from the comprehensive visions, and demands, for modern architecture and urban planning.

The phrase 'landscape urbanism' first appeared in the work of Peter Connolly, a Masters of Urban Design student from RMIT Melbourne. In 1994, Connolly used the phrase in the title for his Masters of Urban Design proposal at RMIT Melbourne. Here, he suggested that 'a language of "landscape urbanism" barely exists and needs articulating', and that 'existing urbanisms ... are limited in the exploration of the landscape'. He also used the term 'landscape as urbanism' in his 1994 essay, '101 Ideas About Big Parks'. In 1996 Tom Turner wrote that

The city of the future will be an infinite series of landscapes: psychological and physical, urban and rural, flowing apart and together. They will be mapped and planned for special purposes, with the results recorded in geographical information systems (GIS), which have the power to construct and retrieve innumerable plans, images and other records. Christopher Alexander was right: a city is not a tree. It is a landscape.

In the late 1990s, concepts of 'landscape urbanism' were often used by landscape architects in the United States in the re-organisation of declining post-industrial cities, such as Detroit. From the 2000s, it was used in Europe by architects to mean a highly flexible way of integrating large-scale infrastructure, housing and open space. By the late 2000s, the phrase became associated with highly commercialized, multi-phase urban parks, such as Olympic park design. Landscape urbanism strategies in the U.S. are now widely used in waterfront redevelopment, recapturing urban vacancy, urban agriculture, and green infrastructure. LU, EU, and IU strategies are rising in importance with growing concerns over climate change.

History

The first major event to do with 'landscape urbanism' was the Landscape Urbanism conference sponsored by the Graham Foundation in Chicago in April 1997. Speakers included Charles Waldheim, Mohsen Mostafavi, James Corner of James Corner/Field Operations, Alex Wall, and Adriaan Geuze of the firm West 8, among others. The formative period of Landscape Urbanism can be traced back to RMIT University and University of Pennsylvania in the late 1980s, at a time when Peter Connolly, Richard Weller, James Corner, Mohsen Mostafavi, and others were exploring the artificial boundaries of Landscape Architecture, Urban Design and Architecture, searching for better ways to deal with complex urban projects. However, their texts cite and synthesize the ideas of influential modernist methods, programmes and manifestoes that appeared in the early twentieth century. Charles Waldheim, Anu Mathur, Alan Berger, Chris Reed, amongst others, were students at the University of Pennsylvania during this formative period for Landscape Urbanism. After the Chicago conference, European design schools and North American design institutions formed academic programs and began to formalize a field of Landscape Urbanism studies, including the University of Toronto, Harvard Graduate School of Design, Oslo School of Architecture, Massachusetts Institute of Technology, Catholic University in Leuven, Belgium, the University of Illinois at Chicago, and London's Architectural Association. 

The development of an actual operative response to the broad and often vague concepts surrounding landscape urbanism was largely developed at the Architectural Association in London. Prior to this period of design exploration, landscape urbanism had never been clearly developed as an actual design practice. Today, much of the design culture that has come to be associated with landscape urbanism was initiated and developed in the AA Landscape Urbanism program during its early formative period and its influence persists in many educational institutions. A number of practices that have chosen to adopt the design and conceptual approach towards urbanism have also adopted many of these design strategies.

Themes

James Corner is the author of an essay entitled "Terra Fluxus." He has identified four general ideas that are important for use in Landscape Urbanism. They are as follows: 

1. Process over time - Understanding the fluid or changing nature of any environment and the processes that affect change over time. A respect for natural processes (Ecology) - the idea that our lives intertwine with the environment around us, and we should therefore respect this when creating an urban environment. Landscape Urbanism is concerned with a working surface over time – a type of urbanism that anticipates change, open endedness and negotiation.
2. Horizontality - The use of horizontal alignment in landscaping, rather than relying on vertical structuring.
3. Working Methods /Techniques - Those who practice the idea of landscape urbanism should be able to adapt their techniques to the environment that they are in.
4. The imaginary - That in many ways the failing of twentieth century planning can be attributed to the absolute impoverishment of the imagination to extend new relationships and sets of possibilities 

Ten characteristics

Tom Turner summarized the ten characteristics of landscape urbanism in the book Landscape design history and theory: landscape architecture and garden design origins:

1. Broad scale context: Landscape urbanism does not belong to a specific scale. It can be considered in small or large-scale projects.
2. Landscape is a context which contains architecture and civil engineering.
3. Landscape is seen as a third machinery arm that makes a connection between its components. Mohsen Mostafavi, the author of Landscape Urbanism : A Manual for the Machinic Landscape used the same phrase.
4. LU projects can provide the opportunity of increasing the social interactions. Also, Emily Talen, one of the writers of Landscape Urbanism and its Discontentes talks about social aspects of a LU project "by forming three theoretical alliances: one with post-structuralism, one with ecology, and one --peculiarly-- with Marxism."
5. Function is the most significant concern in LU machine, which gives the appearance of a project less importance.
6. LU discovers the potentials and opportunities in landscapes.
7. The infrastructure are highlighted in LU projects.
8. LU projects will develop the interrelationship between natural and engineered systems.
9. LU will break the boundary between the landscape and the city and will organize them as one.
10. The answer to the projects which are complex or have ecological concentrations, is landscape urbanism

Projects

The following are Landscape Urbanism projects that are available that can provide more information about the theory in practice:

• Madrid Rio, Ginés Garrido [Director] Burgos & Garrido / Porras La Casta / Rubio A.Sala / West 8
• Fresh Kills Landfill Competition, Field Operations/James Corner
• The High Line, Field Operations/James Corner
• Downsview Park Competition, all finalist entries 
• Schouwburgplein, Rotterdam, West 8/Adriaan Geuze
• Also see projects by Stoss/Chris Reed 

Criticism

Landscape urbanism has been criticized as an idea that is only loosely defined from a set of flashy projects. These are expensive schemes with a commercial and esthetic purpose that satisfy a local or regional ambition to invest in ecology or sustainability without posing a more globally applicable approach. A true merger of landscape architecture with the field of Urban Ecology lacks. From this criticism Frederick Steiner introduced landscape ecological urbanism as an approach that can include the field of urban ecology and Wybe Kuitert has shown how such integrative planning and management of the city should rely on analysis. Discerning the potential quality of wild nature in the city is a first step to see how new urban ecology might be developed. Potential vegetation maps for a city are the tool to this end.

One opponent to Landscape Urbanism is New Urbanism, led by Andres Duany, which promotes walkable communities and smart growth with its Transit Oriented Development (TOD) and Traditional Neighborhood Design (TND). In response to landscape urbanism’s focus on expansive green space in urban development, Duany stated that “density and urbanism are not the same.” Further, “unless there is tremendous density, human beings will not walk.”  The result is patches of green sprawl that lose connectivity to the greater network. 

Emo Urbanism is another philosophy critical of Landscape Urbanism. The movement contends that Landscape Urbanism views ecology as an aesthetic element of style and not urban ecology. The artificial ecology replaces the entropic state to re-create a landscape that fits a particular brand or aesthetic. The loss is a dynamic, adaptive, and certainly essential urban system. Emo urbanism differs by making evolving "nature" a key component of the design process. The realization of this process is called “Urbanature" and "Big Nature." As an evolving urban ecology, Charles Morris Anderson has described this connection as the “thinness.” It is the simultaneous perception and implicit understanding of the past, present, and future. Emo Urbanist projects include the built work of Charles Anderson at the Olympic Sculpture Park in Seattle, WA; The Anchorage Museum Common in Anchorage, AK; the yet to be constructed Project Phoenix in Haiti and Hellinikon's Metropolitan Park in Athens, Greece. 

Ian Thompson has published a critical review of landscape urbanism in which he identifies its ten tenets and asks six critical questions. His conclusions are:

... there are ideas with the Landscape Urbanism discourse which have great merit, among which I would include the breaking down of professional distinctions, the integration of ecological thinking, the foregrounding of infrastructure, the interest in the positive use of waste materials and the emphasis upon functionality rather than mere appearance. There is also a quantity of dubious philosophy, unhelpful imagery and obscurantist language that Landscape Urbanism ought to dump. ... Larding the case for Landscape Urbanim with Deleuzian and Derridean references was a mistake, since it was done principally to impress an academic elite, and it has even left large sections of its intended audience bemused'.

Landscape architecture

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Landscape_architecture 

Stourhead in Wiltshire, England, designed by Henry Hoare (1705–1785), "the first landscape gardener, who showed in a single work, genius of the highest order"

 

Landscape architecture is the design of outdoor areas, landmarks, and structures to achieve environmental, social-behavioural, or aesthetic outcomes. It involves the systematic investigation of existing social, ecological, and soil conditions and processes in the landscape, and the design of interventions that will produce the desired outcome. The scope of the profession includes landscape design; site planning; stormwater management; erosion control; environmental restoration; parks, recreation and urban planning; visual resource management; green infrastructure planning and provision; and private estate and residence landscape master planning and design; all at varying scales of design, planning and management. A practitioner in the profession of landscape architecture is called a landscape architect.

Definition of landscape architecture

Landscape architecture is a multi-disciplinary field, incorporating aspects of botany, horticulture, the fine arts, architecture, industrial design, soil sciences, environmental psychology, geography, ecology, civil engineering and urban design. The activities of a landscape architect can range from the creation of public parks and parkways to site planning for campuses and corporate office parks, from the design of residential estates to the design of civil infrastructure and the management of large wilderness areas or reclamation of degraded landscapes such as mines or landfills. Landscape architects work on structures and external spaces with limitations toward the landscape or park aspect of the design – large or small, urban, suburban and rural, and with "hard" (built) and "soft" (planted) materials, while integrating ecological sustainability. The most valuable contribution can be made at the first stage of a project to generate ideas with technical understanding and creative flair for the design, organization, and use of spaces. The landscape architect can conceive the overall concept and prepare the master plan, from which detailed design drawings and technical specifications are prepared. They can also review proposals to authorize and supervise contracts for the construction work. Other skills include preparing design impact assessments, conducting environmental assessments and audits, and serving as an expert witness at inquiries on land use issues. Landscape architects will focus on planning the gardens on how will they look and what will have to be done.

Education

Landscape Architects are required to take four to five years of college to get a degree on the field. Must know how to create projects from scratch, such as residential or commercial planting and designing outdoor living spaces. Are willing to work with others to get a better outcome for the customers when doing a project.

Field of Study	Landscape Architect
Degree Required	Bachelors or Masters
Yearly income	$75,000+

History

Orangery at the Palace of Versailles, outside Paris

For the period before 1800, the history of landscape gardening (later called landscape architecture) is largely that of master planning and garden design for manor houses, palaces and royal properties, religious complexes, and centers of government. An example is the extensive work by André Le Nôtre for King Louis XIV of France at the Palace of Versailles. The first person to write of making a landscape was Joseph Addison in 1712. The term landscape architecture was invented by Gilbert Laing Meason in 1828, and John Claudius Loudon (1783–1843) was instrumental in the adoption of the term landscape architecture by the modern profession. He took up the term from Meason and gave it publicity in his Encyclopedias and in his 1840 book on the Landscape Gardening and Landscape Architecture of the Late Humphry Repton.

The practice of landscape architecture spread from the Old to the New World. The term "landscape architect" was used as a professional title by Frederick Law Olmsted in the United States in 1863^{[citation needed]} and Andrew Jackson Downing, another early American landscape designer, was editor of The Horticulturist magazine (1846–52). In 1841 his first book, A Treatise on the Theory and Practice of Landscape Gardening, Adapted to North America, was published to a great success; it was the first book of its kind published in the United States. During the latter 19th century, the term landscape architect begun to be used by professional landscapes designers, and was firmly established after Frederick Law Olmsted, Jr. and Beatrix Jones (later Farrand) with others founded the American Society of Landscape Architects (ASLA) in 1899. IFLA was founded at Cambridge, England, in 1948 with Sir Geoffrey Jellicoe as its first president, representing 15 countries from Europe and North America. Later, in 1978, IFLA's Headquarters were established in Versailles.

Fields of activity

Royal Botanic Gardens, Kew, London, established 1759
The Palm House built 1844–1848 by Richard Turner to Decimus Burton's designs

 

Urban design in city squares. Water feature in London, by Tadao Ando who also works with landscapes and gardens

 

The variety of the professional tasks that landscape architects collaborate on is very broad, but some examples of project types include:

• Parks of general design and public infrastructure
• Sustainable development
• Stormwater management including rain gardens, green roofs, groundwater recharge, green infrastructure, and constructed wetlands.
• Landscape design for educational function and site design for public institutions and government facilities
• Parks, botanical gardens, arboretums, greenways, and nature preserves
• Recreation facilities, such as playgrounds, golf courses, theme parks and sports facilities
• Housing areas, industrial parks and commercial developments
• Estate and residence landscape planning and design
• Landscaping and accents on highways, transportation structures, bridges, and transit corridors
• Contributions to urban design, town and city squares, waterfronts, pedestrian schemes
• Natural park, tourist destination, and recreating historical landscapes, and historic garden appraisal and conservation studies
• Reservoirs, dams, power stations, reclamation of extractive industry applications or major industrial projects and mitigation
• Environmental assessment and landscape assessment, planning advice and land management proposals.
• Coastal and offshore developments and mitigation
• Ecological design (any aspect of design that minimizes environmentally destructive impacts by integrating itself with natural processes and sustainability)

Landscape managers use their knowledge of landscape processes to advise on the long-term care and development of the landscape. They often work in forestry, nature conservation and agriculture. 

Landscape scientists have specialist skills such as soil science, hydrology, geomorphology or botany that they relate to the practical problems of landscape work. Their projects can range from site surveys to the ecological assessment of broad areas for planning or management purposes. They may also report on the impact of development or the importance of particular species in a given area.

Landscape planners are concerned with landscape planning for the location, scenic, ecological and recreational aspects of urban, rural and coastal land use. Their work is embodied in written statements of policy and strategy, and their remit includes master planning for new developments, landscape evaluations and assessments, and preparing countryside management or policy plans. Some may also apply an additional specialism such as landscape archaeology or law to the process of landscape planning. 

Green roof (or more specifically, vegetative roof) designers design extensive and intensive roof gardens for storm water management, evapo-transpirative cooling, sustainable architecture, aesthetics, and habitat creation.

Relation to urban planning

The combination of the traditional landscape gardening and the emerging city planning combined together gave landscape architecture its unique focus. Frederick Law Olmsted used the term 'landscape architecture' using the word as a profession for the first time when designing the Central Park.

 

Through the 19th century, urban planning became a focal point and central issue in cities. The combination of the tradition of landscape gardening and the emerging field of urban planning offered landscape architecture an opportunity to serve these needs. In the second half of the century, Frederick Law Olmsted completed a series of parks which continue to have a significant influence on the practices of landscape architecture today. Among these were Central Park in New York City, Prospect Park in Brooklyn, New York and Boston's Emerald Necklace park system. Jens Jensen designed sophisticated and naturalistic urban and regional parks for Chicago, Illinois, and private estates for the Ford family including Fair Lane and Gaukler Point. One of the original eleven founding members of the American Society of Landscape Architects (ASLA), and the only woman, was Beatrix Farrand. She was design consultant for over a dozen universities including: Princeton in Princeton, New Jersey; Yale in New Haven, Connecticut; and the Arnold Arboretum for Harvard in Boston, Massachusetts. Her numerous private estate projects include the landmark Dumbarton Oaks in the Georgetown neighborhood of Washington, D.C. Since that time, other architects – most notably Ruth Havey and Alden Hopkins – changed certain elements of the Farrand design. 

Since this period urban planning has developed into a separate independent profession that has incorporated important contributions from other fields such as civil engineering, architecture and public administration. Urban Planners are qualified to perform tasks independent of landscape architects, and in general, the curriculum of landscape architecture programs do not prepare students to become urban planners.

Landscape architecture continues to develop as a design discipline, and to respond to the various movements in architecture and design throughout the 20th and 21st centuries. Thomas Church was a mid-century landscape architect significant in the profession. Roberto Burle Marx in Brazil combined the International style and native Brazilian plants and culture for a new aesthetic. Innovation continues today solving challenging problems with contemporary design solutions for master planning, landscapes, and gardens. 

Ian McHarg was known for introducing environmental concerns in landscape architecture. He popularized a system of analyzing the layers of a site in order to compile a complete understanding of the qualitative attributes of a place. This system became the foundation of today's Geographic Information Systems (GIS). McHarg would give every qualitative aspect of the site a layer, such as the history, hydrology, topography, vegetation, etc. GIS software is ubiquitously used in the landscape architecture profession today to analyze materials in and on the Earth's surface and is similarly used by urban planners, geographers, forestry and natural resources professionals, etc.

Profession

In many countries, a professional institute, comprising members of the professional community, exists in order to protect the standing of the profession and promote its interests, and sometimes also regulate the practice of landscape architecture. The standard and strength of legal regulations governing landscape architecture practice varies from nation to nation, with some requiring licensure in order to practice; and some having little or no regulation. In Europe, North America, parts of South America, Australia, India, and New Zealand, landscape architecture is a regulated profession.

Argentina

Since 1889, with the arrival of the French architect and urbanist landscaper Carlos Thays, recommended to recreate the National Capital's parks and public gardens, it was consolidated an apprentice and training program in landscaping that eventually became a regulated profession, currently the leading academic institution is the UBA University of Buenos Aires"UBA Facultad de Arquitectura, Diseño y Urbanismo" (Faculty of Architecture, Design and Urbanism) offering a Bacherlor’s degree in Urban Landscaping Design and Planning, the profession itself is regulated by the National Ministry of Urban Planning of Argentina and the Institute of the Buenos Aires Botanical Garden.

Australia

The Australian Institute of Landscape Architects (AILA) provides accreditation of university degrees and non statutory professional registration for landscape architects. Once recognized by AILA, landscape architects use the title 'Registered Landscape Architect' across the six states and territories within Australia. 

AILA's system of professional recognition is a national system overseen by the AILA National Office in Canberra. To apply for AILA Registration, an applicant usually needs to satisfy a number of pre-requisites, including university qualification, a minimum number years of practice and a record of professional experience.

Landscape Architecture within Australia covers a broad spectrum of planning, design, management and research. From specialist design services for government and private sector developments through to specialist professional advice as an expert witness.

Canada

In Canada, landscape architecture, like law and medicine, is a self-regulating profession pursuant to provincial statute. For example, Ontario's profession is governed by the Ontario Association of Landscape Architects pursuant to the Ontario Association of Landscape Architects Act. Landscape architects in Ontario, British Columbia, and Alberta must complete the specified components of L.A.R.E (Landscape Architecture Registration Examination) as a prerequisite to full professional standing. 

Provincial regulatory bodies are members of a national organization, the Canadian Society of Landscape Architects / L'Association des Architectes Paysagistes du Canada (CSLA-AAPC), and individual membership in the CSLA-AAPC is obtained through joining one of the provincial or territorial components.

Indonesia

ISLA (Indonesia Society of Landscape Architects) is the Indonesian society for professional landscape architects formed in 4th February 1978 and is a member of IFLA APR and IFLA World. The main aim is increase the dignity of the professional members of landscape architects by increasing their activity role in community service, national and international development. The management of IALI consists of National Administrators who are supported by 20 Regional Administrators (Provincial level) and 3 Branch Managers at city level throughout Indonesia.

Landscape architecture education in Indonesia was held in 18 universities, which graduated D3, Bachelor and Magister graduates. The landscape architecture education incorporate in Association of Indonesian Landscape Architecture Education.

Italy

AIAPP (Associazione Italiana Architettura del Paesaggio) is the Italian association of professional landscape architects formed in 1950 and is a member of IFLA and IFLA Europe (formerly known as EFLA). AIAPP is in the process of contesting this new law which has given the Architects' Association the new title of Architects, Landscape Architects, Planners and Conservationists whether or not they have had any training or experience in any of these fields other than Architecture. In Italy, there are several different professions involved in landscape architecture:

• Architects
• Landscape designers
• Doctor landscape agronomists and Doctor landscape foresters, often called Landscape agronomists.
• Agrarian Experts and Graduated Agrarian experts.

New Zealand

The New Zealand Institute of Landscape Architects (NZILA) is the professional body for Landscape Architects in NZ www.nzila.co.nz.

In April 2013, NZILA jointly with AILA, hosted the 50th International Federation of Landscape Architects (IFLA) World Congress in Auckland, New Zealand. The World Congress is an international conference where Landscape Architects from all around the globe meet to share ideas around a particular topic.

Within NZ, Members of NZILA when they achieve their professional standing, can use the title Registered Landscape Architect NZILA.

NZILA provides an education policy and an accreditation process to review education programme providers; currently there are three accredited undergraduate Landscape Architecture programmes in New Zealand. Lincoln University also has an accredited masters programme in landscape architecture.

Republic of Ireland

The Irish Landscape Institute [ILI] (www.irishlandscapeinstitute.com) is the officially recognized (by the Irish State) professional body representing landscape architects and parks professionals, in both the Republic of Ireland and Northern Ireland. The ILI was formed in 1992 by the merger of the ILHI (Institute of Landscape Horticulture of Ireland) and the IILA (Irish Institute of Landscape Architects), representing the related disciplines of landscape architecture and landscape horticulture. The Institute currently (October 2017) has a total membership of 160 (approx.) within 7 membership categories (student, graduate, affiliate, parks professional, corporate, fellow, honorary). In the absence of state regulation of the profession or title 'landscape architect', ILI is self-regulating, as for example in its adoption of the trade-marked title, 'Registered Landscape Architect', that is solely permissible for use by corporate members.

At international level, the ILI is a full member of the International Federation of Landscape Architects (IFLA) through its European Region (IFLA-Europe). The ILI has play a consistent and active role in IFLA and the current president of IFLA-Europe is Irishman and ILI Past President, Mr. Tony Williams MILI. In the Republic of Ireland, the ILI is a member institute of the Urban Forum, which represents 5 built-environment professional bodies in engineering, architecture, planning, quantity surveying and landscape architecture.

ILI promotes the landscape profession by its accreditation of the master's degree programme in University College Dublin, its certification of Continuing Professional Development (CPD) for its members, administration of professional practice examinations, advocacy and lobbying in respect of government policies, guidelines and standards (e.g. the National Landscape Strategy, National Planning Framework, Blue-Green Infrastructure), conferences and seminars, public lectures and design awards.

The profession grew rapidly during the Irish economic boom of the early 21st. century, benefiting from the upsurge in the construction and development sectors and from the States' capital investment in infrastructure. The recession brought a sharp reduction in membership numbers. The profession and ILI has proven resilient with clear evidence of a slow but steady recovery through growth in membership and in employment, since the commencement of economic recovery in 2014.

A key challenge remains: there is still no professional regulation or protection registration of title in Ireland, despite calls for such on successive government by ILI over many years. Therefore, there is no state-guarantee or protection of clients, for example in terms of insuring and verifying educational qualifications, professional indemnity insurance or Continuing Professional Development (CPD) of those claiming to be landscape architects. Notwithstanding this, there is a growing awareness in some important sectors (e.g. government departments, media, construction, tourism) of the profession. This is due - to some degree - to the ongoing work of the ILI in promoting the benefits of landscape architecture to Irish society, economy and environment.

Landscape architects in Ireland work in private practice, public sector bodies at local government level and in some state bodies (e.g. transport, national heritage) and in academia. The demand for their professional services is often associated with public infrastructure projects (e.g. roads, motorways, renewable energy facilities, water treatment plants, etc.), Blue-Green Infrastructure (planning, design and management of parks, greenspaces, amenity trees) and with construction projects related to land use developments, principally residential, commercial and mixed-use developments in urban landscapes. 

Landscape architects are employed in design of: green infrastructure, public realm, institutional/medical/industrial campuses and settings, parks, play facilities, transport (road/rail/cycle/port) corridors, retail complexes, residential estates (including plans for remediation of now-abandoned housing 'ghost' estates), village improvements, accessibility audits, graveyard restoration schemes, wind farms, wetland drainage systems and coastal zones. They are also significantly employed in preparation/review of statutory impact assessment reports on landscape, visual and ecological impacts of planning proposals.

Norway

Landscape architecture in Norway was established in 1919 at the Norwegian University of Life Sciences (NMBU) at Ås. The Norwegian School of Landscape Architecture at the Faculty of Landscape and Society is responsible for Europe's oldest landscape architecture education on an academic level. The departments areas include design and design of cities and places, garden art history, landscape engineering, greenery, zone planning, site development, place making and place keeping.

South Africa

In May 1962, Joane Pim, Ann Sutton, Peter Leutscher and Roelf Botha (considered the forefathers of the profession in South Africa) established the Institute for Landscape Architects, now known as the Institute for Landscape Architecture in South Africa (ILASA). ILASA is a voluntary organisation registered with the South African Council for the Landscape Architectural Profession (SACLAP). It consists of three regional bodies, namely, Gauteng, KwaZula-Natal and the Western Cape. ILASA’s mission is to advance the profession of landscape architecture and uphold high standards of professional service to its members, and to represent the profession of landscape architecture in any matter which may affect the interests of the members of the Institute. ILASA holds the country’s membership with The International Federation of Landscape Architects (IFLA).

In South Africa, the profession is regulated by SACLAP, established as a statutory council in terms of Section 2 of the South African Council for the Landscape Architectural Profession Act – Act 45 of 2000. The Council evolved out of the Board of Control for Landscape Architects (BOCLASA), which functioned under the Council of Architects in terms of The Architectural Act, Act 73 of 1970. SACLAP’s mission is to establish, direct, sustain and ensure a high level of professional responsibilities and ethical conduct within the art and science of landscape architecture with honesty, dignity and integrity in the broad interest of public health, safety and welfare of the community. 

After completion of an accredited under-graduate and/or post-graduate qualification in landscape architecture at either the University of Cape Town or the University of Pretoria, or landscape technology at the Cape Peninsula University of Technology, professional registration is attained via a mandatory mentored candidacy period (minimum of two years) and sitting of the professional registration exam. After successfully completing the exam, the individual is entitled to the status of Professional Landscape Architect or Professional Landscape Technologist.

United Kingdom

The UK's professional body is the Landscape Institute (LI). It is a chartered body which accredits landscape professionals and university courses. At present there are fifteen accredited programmes in the UK. Membership of the LI is available to students, academics and professionals, and there are over 3,000 professionally qualified members.

The Institute provides services to assist members including support and promotion of the work of landscape architects; information and guidance to the public and industry about the specific expertise offered by those in the profession; and training and educational advice to students and professionals looking to build upon their experience.

In 2008, the LI launched a major recruitment drive entitled "I want to be a Landscape Architect" to encourage the study of Landscape Architecture. The campaign aimed to raise the profile of landscape architecture and highlight its valuable role in building sustainable communities and fighting climate change.

As of July 2018, the "I want to be a Landscape Architect" initiative was replaced by a brand new careers campaign entitled #ChooseLandscape, which aims to raise awareness of landscape as a profession; improve and increase access to landscape education; and inspire young people to choose landscape as a career. This new campaign includes other landscape-related professions such as landscape management, landscape planning, landscape science and urban design.

United States

In the United States, Landscape Architecture is regulated by individual state governments. For a landscape architect, obtaining licensure requires advanced education and work experience, plus passage of the national examination called The Landscape Architect Registration Examination (L.A.R.E.). Several states require passage of a state exam as well. In the United States licensing is overseen both at the state level, and nationally by the Council of Landscape Architectural Registration Boards (CLARB). Landscape architecture has been identified as an above-average growth profession by the US Bureau of Labor Statistics and was listed in U.S. News & World Report's list of Best Jobs to Have in 2006, 2007, 2008, 2009 and 2010. The national trade association for United States landscape architects is the American Society of Landscape Architects. Frederic Law Olmsted, who designed Central Park in New York City, is known as the "father of American Landscape Architecture."