PK¨©ML•ˆp
codemeta.json{"@context": ["https://doi.org/doi:10.5063/schema/codemeta-2.0", "http://schema.org"], "@type": "SoftwareSourceCode", "provider": {"url": "https://www.comses.net", "@type": "Organization", "name": "CoMSES Network (CoMSES)", "@id": "https://www.comses.net"}}PK¨©MLOğÓR`R`docs/ssas.3_3D.nlogo; This is a re-implementation of the model described in
; Gilbert, Nigel. (1997). A simulation of the structure of academic science.
; Sociological Research Online, 2(2)3, http://www.socresonline.org.uk/2/2/3.html.
;
; The original model was written in Common Lisp in 1996 and run using Macintosh Common Lisp
; This version is for NetLogo 4.1, 3D version and was writtin on 19 May 2010, mainly in
; in a Boeing 777 over the Atlantic.
; The re-implementation stays fairly close to the original logic, which is why it does not
; follow normal NetLogo style in some places.
; December 2010: added correction to procedure 'original' to use direct-distance rather than
; in-radius and to use a constant that converts from the 'old' distance metric to the new.
; Bug found by Nicholas Payette , to whom many thanks.
; The NetLogo grid is used as the 'universe' of knowledge, with the z axis representing time
; the papers are reepresented as dots coloured the same as their 'generator' papers. (This
; is a deviation from the original, which was in black and white).
; The original used a universe measuring 2^16 - 1 by 2^16 - 1 units, but the units were
; discrete. This is mapped in this re-implementation to the NetLogo grid, set to 33 by 33
; patches, but measured in floating-point (actually double) coordinates.
globals [ distance-conversion-factor ]
breed [ papers paper ]
papers-own [
my-author
date
cited-papers
]
breed [ authors author ]
authors-own [
birth
death
n-citations
my-papers
]
to setup
clear-all
set distance-conversion-factor (max-pxcor - min-pxcor + 1) / 2 ^ 16
set-default-shape papers "dot"
repeat 1000 [ initial-papers ]
end
to initial-papers
create-papers 1 [
hide-turtle
set date 0
setxyz random-xcor random-ycor 0
set cited-papers []
set my-author ifelse-value (count authors > 0 and random 100 > alpha)
[ one-of authors ]
[ create-new-author ]
ask my-author [ set my-papers fput myself my-papers ]
]
end
to-report create-new-author
let new-author nobody
hatch-authors 1 [
hide-turtle
set birth ticks
set death ticks + random phi
set my-papers []
set new-author self
]
report new-author
end
to go
if ticks = 1000 [ stop ]
repeat 1 + floor ( omega * (count papers - 1000) + ((random 100) - 50) / 100) [
; keep trying to create a new paper until we write a paper that is original
let original? false
while [ not original? ] [
let generator-paper select-generator-paper
let new-paper nobody
let prob 1
create-papers 1 [
set color [color] of generator-paper
set size 0.5
set date ticks
; the z coordinate factor ensures that after 1000 ticks the papers are placed at the
; end of the z axis
setxyz [ xcor ] of generator-paper [ ycor ] of generator-paper ticks * max-pzcor / 1000
set new-paper self
set cited-papers []
]
let near-papers nearby-papers new-paper
let cited-paper one-of near-papers
while [ prob <= 100 and is-paper? cited-paper ] [
set near-papers near-papers with [ self != cited-paper ]
ask new-paper [
set cited-papers fput cited-paper cited-papers
mix cited-paper prob
]
set prob prob + random beta
set cited-paper one-of near-papers
]
ask new-paper [
set original? original
ifelse original?
[ store-paper generator-paper]
[ die ]
]
]
]
do-plots
tick
end
; choose a paper with an author that is still alive
to-report select-generator-paper
report one-of papers with [ ticks <= [death] of my-author ]
end
; return an agentset of papers that are 'near' to the new-paper in knowledge space
to-report nearby-papers [ new-paper ]
let near-papers nobody
ask new-paper [
set near-papers other papers with [ direct-distance myself <= (epsilon * distance-conversion-factor) ]
]
report near-papers
end
; does the same as 'in-radius', but doesn't wrap around as the built-in primitive does
to-report direct-distance [ other-paper ]
report sqrt (([xcor] of other-paper - xcor) ^ 2 + ([ycor] of other-paper - ycor) ^ 2)
end
; move myself so that I am a bit closer to 'citation'
to mix [ citation prob ] ; paper procedure
setxyz
xcor + round (([xcor] of citation - xcor ) * ((100 - prob) / 200 ))
ycor + round (([ycor] of citation - ycor ) * ((100 - prob) / 200 ))
zcor
end
; report true if there are no other papers near to me
to-report original ; paper procedure
report not any? other papers with [ direct-distance myself <= (delta * distance-conversion-factor) ]
end
; give the paper an author and record citations
to store-paper [ generator-paper ] ; paper procedure
set my-author ifelse-value ((random 100) > alpha)
[ [my-author] of generator-paper ]
[ create-new-author ]
ask my-author [ set my-papers fput myself my-papers ]
foreach cited-papers [
ask ? [ increment-citations ]
]
end
to increment-citations ; paper procedure
ask my-author [
set n-citations n-citations + 1
]
end
to do-plots
set-current-plot "Cumulative papers"
plot count papers with [ date > 0 ]
set-current-plot "References per paper"
histogram [length cited-papers] of papers with [ date > 0 ]
set-current-plot "Citations per author"
histogram [n-citations] of authors
set-current-plot "Papers per author"
histogram [length my-papers] of authors
end
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@#$#@#$#@
WHAT IS IT?
-----------
Contemporary science exhibits a number of regularities in the relationships between quantitative indicators of its growth. The classic source for these relationships is de Solla Price's (1963) lectures on Little Science, Big Science, in which he argues that there is evidence of a qualitative change in science from traditional 'little' science to the big science of large research teams and expensive research equipment. In making this argument, de Solla Price summarizes well what was then known about the structure of 'little' science. In the following thirty years, the dramatic changes which de Solla Price envisaged have generally not occurred (with some exceptions) and his summary is therefore still useful.
The central theme of de Solla Price's book is that science is growing exponentially, with a doubling time of between 10 and 20 years, depending on the indicator. For him, the fundamental characteristic of science is the publication of research papers in academic journals. He notes that papers always include references to other papers in the scientific literature, with a mean of 10 references per paper. The number of journals has followed an exponential growth curve with a doubling every 15 years since the mid-eighteenth century. There is approximately one journal for every 100 scientists (where a scientist is someone who has published a scientific paper) and scientists divide themselves up into 'invisible colleges' of roughly this size.
References tend to be to the most recent literature. Half of the references made in a large sample of papers would be to other papers published not more than 9 to 15 years previously. However, because the number of papers is growing exponentially, every paper has on average an approximately equal chance of being cited, although there are large variations in the number of citations different papers receive.
These observed regularities constitute the criteria with which to judge the simulation. The task is to develop a model which will reproduce these regularities from a small set of plausible assumptions.
HOW IT WORKS
------------
At the heart of the model is the idea that science as an institution can be characterized by 'papers', each proposing a new quantum of knowledge, and 'authors' who write papers. The simulation will model the generation of papers by authors.
The first assumption we make is that the simulation may proceed without reference to any external 'objective reality'. We shall simulate scientific papers each of which will capture some quantum of 'knowledge', but the constraints on this knowledge will be entirely internal to the model. To represent a quantum of knowledge, we shall use a sequence of bits. The bit sequences representing quanta of knowledge will be called 'kenes', a neologism intentionally similar to 'genes'.
Kenes could in principal consist of arbitrary bit sequences of indefinite length. However, we shall want to portray 'science' graphically in a convenient fashion and this means locating kenes in space. Since arbitrary bit sequences can only be mapped into spaces of indefinite dimensionality, we impose a rather strict limit on which sequences are allowable, purely for the purposes of permitting graphical displays. We require that each kene is composed of two sub- sequences of equal length, and we treat each sub-sequence as a representation of a coordinate on a plane. This restriction on kenes is substantial, but does not affect the logic of the simulation while making it much easier to see what is going on. It should be emphasized that the requirement that kenes can be mapped into a plane is not part of the model of the structure of science and could be relaxed in further work.
As a consequence of the fact that kenes can be decomposed into two coordinates, every kene can be assigned a position on the plane. Since each paper contains knowledge represented by one kene, that kene can stand for the paper and in particular, papers can also be located on the plane. In the simulation, each kene is composed of two coordinates, each 16 bits in length, giving a total 'scientific universe' of 2162 = 4,294,967,296 potential kenes, that is, an essentially infinite number compared with the number of papers generated during one run of the simulation. Authors can also be positioned on the plane according to the location of their latest paper.
One of the principal constraints on publication in science is that no two papers may be published which contain the same or similar knowledge. This amounts to the requirement that no two papers have identical kenes. In the model we extend this to require that no two papers have kenes which are 'similar', where similarity is measured by the distance between the kenes (a paper is deemed original if it lies more than delta coordinate units away from any other paper, where delta and the other Greek symbols below are numerical parameters set at the start of the simulation). Since distance is a well defined notion even in multi-dimensional space, the idea that kenes and thus papers can be close does not depend on the requirement that kenes must be located on a plane.
So far, we have defined the three essential entities in the model: papers, authors and kenes. Next we need to consider the basic processes which give rise to these entities.
We propose that it is papers which give rise to further papers, with authors adopting only an incidental role in the process. A 'generator' paper is selected at random from those papers already published whose authors are still active in science. This spawns a new potential paper as a copy of itself, with the same kene. The new paper then selects a set of other papers to cite by randomly choosing papers located within the region of its generator paper (the 'region' is defined as the area within a circleofradius epsilon. Each of the cited papers modifies the generator kene to some extent. The first such paper has the most influence on the paper's kene, with successive citations having a decreasing effect. A spatial way of thinking about the process is that each cited paper 'pulls' the kene from its original location some way towards the location of the cited kene.
More precisely, the x coordinate of the new paper (p) is affected by the cited paper (c) thus:
x'p = xp + (xc - xp) * (1 - m) / 2
where m is a value between zero and one which increases randomly but monotonically for each successive citation. A similar equation determines the new y coordinate.
The result is a kene which is somewhat changed compared with the generator kene. If the changes are sufficient, the new kene will no longer be close to the generator kene. If the new kene is also not close to the kene of any previously published paper, it can be considered to be original and can be 'published'. If, however, the new kene is similar to a previous paper, the publication is abandoned.
Thus papers generate new papers which combine the influence of the generator paper with the papers it cites. Finally, publishable papers choose an author. A proportion (alpha) of papers choose a new, previously unpublished author and the rest are assigned the author of the generator paper.
An increasing number of papers are generated at each time step since there is a small constant probability, omega, of each published paper acting as a generator for a further paper at the next time step.
The rules concerning authors are much simpler. Authors remain in science from the time they publish their first paper until retirement. They are modelled as retiring when the duration of their time in science exceeds a value drawn from a uniform distribution from 0 to phi time units.
This section has described the rules which determine the generation of papers and authors in the simulation. It may be noticed that the rules are local and at the 'micro' level. That is, they make no reference to the overall state of the simulation and do not refer to aggregate properties. Papers, for example, cite other papers in their region without reference to whether that locality is relatively dense or thinly spread, or to the positions of papers outside the neighbourhood.
HOW TO USE IT
-------------
This section could explain how to use the model, including a description of each of the items in the interface tab.
THINGS TO NOTICE
----------------
You can pan, move and zoom the 3D plot.
EXTENDING THE MODEL
-------------------
See Watts, C. and Gilbert, N. (forthcoming) in Scientometrics.
NETLOGO FEATURES
----------------
The model requires the 3D version of NetLogo 4.1
CREDITS AND REFERENCES
----------------------
This is a re-implementation of the model described in
Gilbert, Nigel. (1997). A simulation of the structure of academic science.
Sociological Research Online, 2(2)3, http://www.socresonline.org.uk/socresonline/2/2/3.html.
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@#$#@#$#@
NetLogo 3D 4.1.1
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1
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PK¨©MLOğÓR`R`code/ssas.3_3D.nlogo; This is a re-implementation of the model described in
; Gilbert, Nigel. (1997). A simulation of the structure of academic science.
; Sociological Research Online, 2(2)3, http://www.socresonline.org.uk/2/2/3.html.
;
; The original model was written in Common Lisp in 1996 and run using Macintosh Common Lisp
; This version is for NetLogo 4.1, 3D version and was writtin on 19 May 2010, mainly in
; in a Boeing 777 over the Atlantic.
; The re-implementation stays fairly close to the original logic, which is why it does not
; follow normal NetLogo style in some places.
; December 2010: added correction to procedure 'original' to use direct-distance rather than
; in-radius and to use a constant that converts from the 'old' distance metric to the new.
; Bug found by Nicholas Payette , to whom many thanks.
; The NetLogo grid is used as the 'universe' of knowledge, with the z axis representing time
; the papers are reepresented as dots coloured the same as their 'generator' papers. (This
; is a deviation from the original, which was in black and white).
; The original used a universe measuring 2^16 - 1 by 2^16 - 1 units, but the units were
; discrete. This is mapped in this re-implementation to the NetLogo grid, set to 33 by 33
; patches, but measured in floating-point (actually double) coordinates.
globals [ distance-conversion-factor ]
breed [ papers paper ]
papers-own [
my-author
date
cited-papers
]
breed [ authors author ]
authors-own [
birth
death
n-citations
my-papers
]
to setup
clear-all
set distance-conversion-factor (max-pxcor - min-pxcor + 1) / 2 ^ 16
set-default-shape papers "dot"
repeat 1000 [ initial-papers ]
end
to initial-papers
create-papers 1 [
hide-turtle
set date 0
setxyz random-xcor random-ycor 0
set cited-papers []
set my-author ifelse-value (count authors > 0 and random 100 > alpha)
[ one-of authors ]
[ create-new-author ]
ask my-author [ set my-papers fput myself my-papers ]
]
end
to-report create-new-author
let new-author nobody
hatch-authors 1 [
hide-turtle
set birth ticks
set death ticks + random phi
set my-papers []
set new-author self
]
report new-author
end
to go
if ticks = 1000 [ stop ]
repeat 1 + floor ( omega * (count papers - 1000) + ((random 100) - 50) / 100) [
; keep trying to create a new paper until we write a paper that is original
let original? false
while [ not original? ] [
let generator-paper select-generator-paper
let new-paper nobody
let prob 1
create-papers 1 [
set color [color] of generator-paper
set size 0.5
set date ticks
; the z coordinate factor ensures that after 1000 ticks the papers are placed at the
; end of the z axis
setxyz [ xcor ] of generator-paper [ ycor ] of generator-paper ticks * max-pzcor / 1000
set new-paper self
set cited-papers []
]
let near-papers nearby-papers new-paper
let cited-paper one-of near-papers
while [ prob <= 100 and is-paper? cited-paper ] [
set near-papers near-papers with [ self != cited-paper ]
ask new-paper [
set cited-papers fput cited-paper cited-papers
mix cited-paper prob
]
set prob prob + random beta
set cited-paper one-of near-papers
]
ask new-paper [
set original? original
ifelse original?
[ store-paper generator-paper]
[ die ]
]
]
]
do-plots
tick
end
; choose a paper with an author that is still alive
to-report select-generator-paper
report one-of papers with [ ticks <= [death] of my-author ]
end
; return an agentset of papers that are 'near' to the new-paper in knowledge space
to-report nearby-papers [ new-paper ]
let near-papers nobody
ask new-paper [
set near-papers other papers with [ direct-distance myself <= (epsilon * distance-conversion-factor) ]
]
report near-papers
end
; does the same as 'in-radius', but doesn't wrap around as the built-in primitive does
to-report direct-distance [ other-paper ]
report sqrt (([xcor] of other-paper - xcor) ^ 2 + ([ycor] of other-paper - ycor) ^ 2)
end
; move myself so that I am a bit closer to 'citation'
to mix [ citation prob ] ; paper procedure
setxyz
xcor + round (([xcor] of citation - xcor ) * ((100 - prob) / 200 ))
ycor + round (([ycor] of citation - ycor ) * ((100 - prob) / 200 ))
zcor
end
; report true if there are no other papers near to me
to-report original ; paper procedure
report not any? other papers with [ direct-distance myself <= (delta * distance-conversion-factor) ]
end
; give the paper an author and record citations
to store-paper [ generator-paper ] ; paper procedure
set my-author ifelse-value ((random 100) > alpha)
[ [my-author] of generator-paper ]
[ create-new-author ]
ask my-author [ set my-papers fput myself my-papers ]
foreach cited-papers [
ask ? [ increment-citations ]
]
end
to increment-citations ; paper procedure
ask my-author [
set n-citations n-citations + 1
]
end
to do-plots
set-current-plot "Cumulative papers"
plot count papers with [ date > 0 ]
set-current-plot "References per paper"
histogram [length cited-papers] of papers with [ date > 0 ]
set-current-plot "Citations per author"
histogram [n-citations] of authors
set-current-plot "Papers per author"
histogram [length my-papers] of authors
end
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WHAT IS IT?
-----------
Contemporary science exhibits a number of regularities in the relationships between quantitative indicators of its growth. The classic source for these relationships is de Solla Price's (1963) lectures on Little Science, Big Science, in which he argues that there is evidence of a qualitative change in science from traditional 'little' science to the big science of large research teams and expensive research equipment. In making this argument, de Solla Price summarizes well what was then known about the structure of 'little' science. In the following thirty years, the dramatic changes which de Solla Price envisaged have generally not occurred (with some exceptions) and his summary is therefore still useful.
The central theme of de Solla Price's book is that science is growing exponentially, with a doubling time of between 10 and 20 years, depending on the indicator. For him, the fundamental characteristic of science is the publication of research papers in academic journals. He notes that papers always include references to other papers in the scientific literature, with a mean of 10 references per paper. The number of journals has followed an exponential growth curve with a doubling every 15 years since the mid-eighteenth century. There is approximately one journal for every 100 scientists (where a scientist is someone who has published a scientific paper) and scientists divide themselves up into 'invisible colleges' of roughly this size.
References tend to be to the most recent literature. Half of the references made in a large sample of papers would be to other papers published not more than 9 to 15 years previously. However, because the number of papers is growing exponentially, every paper has on average an approximately equal chance of being cited, although there are large variations in the number of citations different papers receive.
These observed regularities constitute the criteria with which to judge the simulation. The task is to develop a model which will reproduce these regularities from a small set of plausible assumptions.
HOW IT WORKS
------------
At the heart of the model is the idea that science as an institution can be characterized by 'papers', each proposing a new quantum of knowledge, and 'authors' who write papers. The simulation will model the generation of papers by authors.
The first assumption we make is that the simulation may proceed without reference to any external 'objective reality'. We shall simulate scientific papers each of which will capture some quantum of 'knowledge', but the constraints on this knowledge will be entirely internal to the model. To represent a quantum of knowledge, we shall use a sequence of bits. The bit sequences representing quanta of knowledge will be called 'kenes', a neologism intentionally similar to 'genes'.
Kenes could in principal consist of arbitrary bit sequences of indefinite length. However, we shall want to portray 'science' graphically in a convenient fashion and this means locating kenes in space. Since arbitrary bit sequences can only be mapped into spaces of indefinite dimensionality, we impose a rather strict limit on which sequences are allowable, purely for the purposes of permitting graphical displays. We require that each kene is composed of two sub- sequences of equal length, and we treat each sub-sequence as a representation of a coordinate on a plane. This restriction on kenes is substantial, but does not affect the logic of the simulation while making it much easier to see what is going on. It should be emphasized that the requirement that kenes can be mapped into a plane is not part of the model of the structure of science and could be relaxed in further work.
As a consequence of the fact that kenes can be decomposed into two coordinates, every kene can be assigned a position on the plane. Since each paper contains knowledge represented by one kene, that kene can stand for the paper and in particular, papers can also be located on the plane. In the simulation, each kene is composed of two coordinates, each 16 bits in length, giving a total 'scientific universe' of 2162 = 4,294,967,296 potential kenes, that is, an essentially infinite number compared with the number of papers generated during one run of the simulation. Authors can also be positioned on the plane according to the location of their latest paper.
One of the principal constraints on publication in science is that no two papers may be published which contain the same or similar knowledge. This amounts to the requirement that no two papers have identical kenes. In the model we extend this to require that no two papers have kenes which are 'similar', where similarity is measured by the distance between the kenes (a paper is deemed original if it lies more than delta coordinate units away from any other paper, where delta and the other Greek symbols below are numerical parameters set at the start of the simulation). Since distance is a well defined notion even in multi-dimensional space, the idea that kenes and thus papers can be close does not depend on the requirement that kenes must be located on a plane.
So far, we have defined the three essential entities in the model: papers, authors and kenes. Next we need to consider the basic processes which give rise to these entities.
We propose that it is papers which give rise to further papers, with authors adopting only an incidental role in the process. A 'generator' paper is selected at random from those papers already published whose authors are still active in science. This spawns a new potential paper as a copy of itself, with the same kene. The new paper then selects a set of other papers to cite by randomly choosing papers located within the region of its generator paper (the 'region' is defined as the area within a circleofradius epsilon. Each of the cited papers modifies the generator kene to some extent. The first such paper has the most influence on the paper's kene, with successive citations having a decreasing effect. A spatial way of thinking about the process is that each cited paper 'pulls' the kene from its original location some way towards the location of the cited kene.
More precisely, the x coordinate of the new paper (p) is affected by the cited paper (c) thus:
x'p = xp + (xc - xp) * (1 - m) / 2
where m is a value between zero and one which increases randomly but monotonically for each successive citation. A similar equation determines the new y coordinate.
The result is a kene which is somewhat changed compared with the generator kene. If the changes are sufficient, the new kene will no longer be close to the generator kene. If the new kene is also not close to the kene of any previously published paper, it can be considered to be original and can be 'published'. If, however, the new kene is similar to a previous paper, the publication is abandoned.
Thus papers generate new papers which combine the influence of the generator paper with the papers it cites. Finally, publishable papers choose an author. A proportion (alpha) of papers choose a new, previously unpublished author and the rest are assigned the author of the generator paper.
An increasing number of papers are generated at each time step since there is a small constant probability, omega, of each published paper acting as a generator for a further paper at the next time step.
The rules concerning authors are much simpler. Authors remain in science from the time they publish their first paper until retirement. They are modelled as retiring when the duration of their time in science exceeds a value drawn from a uniform distribution from 0 to phi time units.
This section has described the rules which determine the generation of papers and authors in the simulation. It may be noticed that the rules are local and at the 'micro' level. That is, they make no reference to the overall state of the simulation and do not refer to aggregate properties. Papers, for example, cite other papers in their region without reference to whether that locality is relatively dense or thinly spread, or to the positions of papers outside the neighbourhood.
HOW TO USE IT
-------------
This section could explain how to use the model, including a description of each of the items in the interface tab.
THINGS TO NOTICE
----------------
You can pan, move and zoom the 3D plot.
EXTENDING THE MODEL
-------------------
See Watts, C. and Gilbert, N. (forthcoming) in Scientometrics.
NETLOGO FEATURES
----------------
The model requires the 3D version of NetLogo 4.1
CREDITS AND REFERENCES
----------------------
This is a re-implementation of the model described in
Gilbert, Nigel. (1997). A simulation of the structure of academic science.
Sociological Research Online, 2(2)3, http://www.socresonline.org.uk/socresonline/2/2/3.html.
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