rSNAPsim Documentation¶
Created on Tue Oct 23 09:42:24 2018
@author: William
-
class
rSNAPsim.
rSNAPsim
¶ The Single Molecule Simulator (SMS) provides a python class for running single molecule mRNA translation simulations
When presented with a valid protein sequence the SMS can find open reading frames and simulate intensity trajectories from translation of the protein with given fluorescent tags.
model description
link to paper here / imagemain functions
-open_seq_file(filepath), opens a txt or .gb file and gets the sequence
-get_orfs(nt_sequence, min_codons), returns open reading frames of a given sequence and a minimum codon length per protein
-get_temporal_proteins(), gets the proteins after get_orfs
-analyze_poi(aa_seq,nt_seq), analyzes the proteins of intrest for codon sensitivity and elongation rates
-__.poi(), class to contain proteins of intrest after analyzed
-run_default(), runs get_orfs, get_temporal proteins, and analyze_poi with the first protien found in the sequence
attributes
gene_sequence_str = string of the nucleotide sequence tag_dict = dictionary with various types of fluorescent tag epitopes
tag_full = dictionary of full tag sequences
aa_keys = amino acid single letter keys
codon_types = flag dictionary of which amino acids are set to Wild-type, fast, or slow
aa_table = dictionary of amino acids
aa_table_r = reverse dictionary (amino acid letters are the keys)
strGeneCopy = dictionary of wild-type tRNA copy numbers
strGeneCopy_fast = dictionary of fast tRNA copy numbers
strGeneCopy_slow = dictionary of slow tRNA copy numbers
slow_codons_value = list of slowest codon tRNA copy numbers
fast_codons_value = list of fastest codon tRNA copy numbers
sensitivity_fast_slow = list of sensitivity for amino acids
poi = Class container for proteins of intrest
orfs = dictionary of open reading frames with keys 1,2,3
seq_str = sequence string
proteins = dictionary of proteins detected in the sequence by ORF
tagged_proteins = dictionary of proteins that were detected and tagged
POI
Protein of intrest has the following attributes:
aa_seq = amino acid sequence
nt_seq = nucleotide sequence
gene_length = length of the gene
tag_length = length of the tags
total_length = total length of the full amino acid sequence
name = name of the gene
tag_types = what types of tags does the protien have
tag_epitopes = type of tags and epitope lists per tag
codon_sensitivity = how sensitive is the protein per amino acid sequence?
CAI = codon activation index
CAI_codons = means of the codon activation
ssa
The ssa container class has the following attributes:
no_ribosomes = number of ribosomes
n_traj = number of trajectories
k = all kelongation rates (calculated from codon sequence)
no_rib_per_mrna = number of ribosomes per mRNA strand on average
rib_density = ribosome density
rib_means = ribosome means
rib_vec = raw ribosome location matrix for each trajectory
intensity_vec = fluorescence intensities
time_vec_fixed = the time vector
start_time = the time the simulation was started
evaluating_inhibitor = was there an inhibitor present?
evaluating_frap = was the simulation subjected to a FRAP test
time_inhibit = the time of the perturbation
autocorr_vec = autocorrelation vector of intensities
mean_autocorr = the average autocorrelations, averaged over trajectories
error_autocorr = the standard deviation of the autocorrelation
dwell_time = how long do the ribosomes stay on the mRNA strand calculated by the simulation
ke_sim = the calculated average elongation rate from the simulations
-
SSA
(k, t_array, inhibit_time=0, FRAP=False, Inhibitor=False)¶ mRNA Translation simulation python implementation
given a propensity vector k, time array to record, and inhibitory conditions, run a single trajectory of translation simulation
The simulation is described here: [PUT LINK HERE TO PAPER]
args
k, propensity vector of size gene length + 2, [initiation rate, Codon dependent rates, completion rate / unbinding rate] for reference the codon dependent rates are refering to the time rate of a ribosome to move on to the next codon
t_array, time points to record the ribosome posistions at
keyword args
inhibit_time, the time to start inhibition assays if FRAP or Inhibitor (harringtonine) == True
FRAP, True or false to apply Fluorescence Recovery After Photobleaching (FRAP) https://en.wikipedia.org/wiki/Fluorescence_recovery_after_photobleaching
Inhibitor, True or false to apply harringtonine at inhibit_time. Harringtonine acts as a protien translation initiation inhibitor
-
analyze_poi
(protein, sequence)¶ Analyzes the protein of intrest and stores it in __.POI
args
protein, amino acid sequence as a string
sequence, nucleotide sequence that goes with the protein
-
analyze_seq_file
(filename)¶ General catch all to run all functions necessary before a SSA and store the first POI found from any given sequence
args
filename a txt or gb file to be read and analyzed
-
codon_usage
(nt_seq)¶ Analyzes codon useage from the nucleotide sequence
args
nt_seq, nucleotide sequence as a stringreturns
codon_sensitivity, a list of codon sensitivity for the nucleotide sequence
cai, cai value
-
elongation_animation
(ti=0, tf=1000, tstep=1000, cell_radius=50, imagesize=5, dpi=90, filename='simulated_cell', ssa_obj=None, fcolor='#00FF00', rnacolor='#FF0000', xkcd=False)¶ function that creates a mrna translation animation
-
geomean
(iterable)¶ geometric mean used for codon sensitivity calculations
-
get_acc2
(data, trunc=False)¶ Get autocorrelation function
NOT multi-tau
-
get_autocorr
(intensity_vec, time_vec, totalSimulationTime, geneLength)¶ returns the autocorrelations
-
get_crosscorr
(iv1, iv2)¶ returns the autocorrelations
-
get_gb_file
(accession_number, savetofile=False)¶ A function to poll genbank given an accession number and pull the relevant gb file
args
accession_number, the accession number of the sequence to find. http://www.nslc.wustl.edu/elgin/genomics/bio4342/1archives/2006/AccReference.pdfkeyword args
savetofile, true or false to save the gb file in the same directory as sms for future use
-
get_k
(nt_seq, k_init, k_elong_mean)¶ returns all propensities for a given nucleotide sequence
args
nt_seq, nucleotide sequence as a string
k_initiation, initiation rate of ribosome binding
k_elong_mean, average rate of elgonation experimentally found
-
get_k_construct
(nt_seq, k_init, k_elong_mean, codon_types=None)¶ Returns the k_elongation rates of a given nucleotide sequence under constructed conditions given some sort of key describing which amino acids are slow, fast or natural
args
nt_seq, nucleotide sequence to get the propensities of
k_init, initiation rate of starting translation
k_elong_mean, average rate of elongation for the protein translation
keyword args
codon_types, a dictonary or identifier determining which amino acids are slow, fast or natural
self.codon_types is an example dictionary for the user to change / utilize, if codon_types is left blank get_k_construct uses this internal dictonary
- ex: codon_types = ‘slow’ or ‘rare’ all amino acids set to slow
codon_types = ‘fast’ or ‘common’ all amino acids set to fast codon_types = ‘natural’ all amino acids set to fast
codon_types = {‘A’:[0], ‘T’:[2]} A set to slow, T set to fast codon_types = {‘rare’:[‘A’,’R’],’common’:[‘L’]} A and R set to slow, L set to fast
-
get_orfs
(nt_seq='', min_codons=80)¶ Returns open reading frames of the nucleotide sequence given
- orfs = {‘1’:[proteins],
- ‘2’:[proteins], ‘3’:[proteins]}
keyword args
nt_seq, nucleotide sequence as a string. If left blank uses the self.sequence_str
min_codons, minimum amount of codons to be considered a protein in the open reading frame
-
get_probvec
()¶ returns the probe vectors (epitope positions by codon position) associated with the tagged sequence stored in POI
returns
probe_vec, cumlative probe intensity vector by codon position. Ex: [0,0,0,0,1,1,1,1,2,2,2,3,3,3 etc]
probe_loc, epitope posistion as a binary vector, 1 for epitope pos, 0 for everything else
-
get_simulated_mov
(ssa_obj, filename, filetype)¶ Create a gif or html file of the simulated circlular cell from any sms ssa object
-
get_temporal_proteins
()¶ gets all the temporal proteins after getting the ORFs
__.tagged_proteins = dictionary with keys of tag types and a list of proteins __.pois = list of proteins of intrest __.pois_seq = list of nucleotide sequences of proteins of sequences __.proteins = dictonary with keys of 1 2 or 3 orfs
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kymograph
(ssa_obj, n_traj, bg_intense=True, show_intense=True, tag=0, show_col=True, col_size=1.5, custom_fig=None, facecolor='white', *args, **kwargs)¶ Constructs a kymograph of ribosome locations
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multitau_acc
(ivec, n, sampling_rate, sample_rate_seconds)¶ Multi-tau acc
-
nt2aa
(nt_seq)¶ Translates nucleotides sequences to amino acid sequences
args
nt_seq, nucleotide sequence as a stringreturns
aa_seq, amino acid sequence as string
-
open_seq_file
(seqfile)¶ Reads a sequence file, either a .txt file or a .gb genbank file
args
seqfile, sequence file either in txt, gb, gbk format
-
simulate_cell
(diffusion_constant, kon, koff, kRNA, kdecay, ti=0, tf=1000, tstep=1000, cell_radius=50, imagesize=5, dpi=90, filename='simulated_cell', ssa_obj=None, fcolor='#00FF00', rnacolor='#FF0000')¶ - [DNA] ==kRNA==> [RNA] <==koff== [RNA*] ==translation simulation==> [Protein]===> null
- // || / || ‘=====kon=====’ || / null
-
ssa_solver
(nt_seq=None, all_k=None, k_elong_mean=10, k_initiation=0.03, probePosition=[], n_traj=100, tf=1000, start_time=0, tstep=1000, time_inhibit=0, evaluating_frap=False, evaluating_inhibitor=False, force_python=False)¶ Solve stochastic simulation algorithms (SSA) for the translation simulation.
keyword args
nt_seq, nucleotide sequence to simulate
all_k, the propensity rates for each codon location (obtained via get_k)
k_elong_mean, average elongation rate to normalize by
k_initiation, rate of mRNA translation initiation
probePosition, binary vector of probe positions, i.e. where the tag epitopes start by codon position
n_traj, number of trajectories
tf, final time point
tstep, number of time steps to record from 0 to tf
time_inhibit, inhibition time of translation either, harringtonine assay or FRAP
evaluating_frap, true or false for evaluating frap assay at time_inhibit
evaluating_inhibitor, true or false for evaluating harringtonine at time_inhibit
returns
ssa_obj, a ssa() class containing the raw ribosome posistions simulated and statistics such as intensity vectors from the SSA trajectory group
-
-
class
rSNAPsim.
poi
¶ Protein of Intrest class
Holds all the information for analyzed proteins


| CONTENTS | PREV | NEXT | Java Remote Method Invocation |
RMI applications are often comprised of two separate programs: a server and a client. A typical server application creates a number of remote objects, makes references to those remote objects accessible, and waits for clients to invoke methods on those remote objects. A typical client application gets a remote reference to one or more remote objects in the server and then invokes methods on them. RMI provides the mechanism by which the server and the client communicate and pass information back and forth. Such an application is sometimes referred to as a distributed object application.Distributed object applications need to:
- Locate remote objects
Applications can use one of two mechanisms to obtain references to remote objects. An application can register its remote objects with RMI's simple naming facility, the
rmiregistry
, or the application can pass and return remote object references as part of its normal operation.
- Communicate with remote objects
Details of communication between remote objects are handled by RMI; to the programmer, remote communication looks like a standard method invocation.
- Load class bytecodes for objects that are passed as parameters or return values
Because RMI allows a caller to pass objects to remote objects, RMI provides the necessary mechanisms for loading an object's code as well as transmitting its data.
The illustration below depicts an RMI distributed application that uses the registry to obtain references to a remote object. The server calls the registry to associate a name with a remote object. The client looks up the remote object by its name in the server's registry and then invokes a method on it. The illustration also shows that the RMI system uses an existing web server to load bytecodes of classes written in the Java programming language, from server to client and from client to server, for objects when needed. RMI can load class bytecodes using any URL protocol (e.g., HTTP, FTP, file, etc.) that is supported by the Java platform.


A Merchant may request a payment by calling the function PaymentRequest supplied by the BitcoinExpress library. A PaymentDetails JSON parameter determines the payment details.
The payment details object must include at least the following keys:
If the payment Coins are acceptable, the PaymentRequest resolves to a PaymentAck, otherwise it is rejected with an error string. The sales page may then use data from the PaymentAck to determine an appropriate next step (e.g. say thank you or link to a new page).
NOTE: the following example calls the /mockPayment Issuer endpoint. This function is provided so that developers may quickly test their payment script before they have a back-end implementation in place.
var paymentDetails = {
currency: "XBT",
amount: 0.0000095,
memo: "The art of asking",
issuers: ["(*.carrotpay.com)"],
merchant_data: "sale999264",
email: {
contact<EMAIL_ADDRESS>receipt: true,
refund: false
},
payment_url: "https://eu.carrotpay.com/Bitcoin-express/v1/issuer/mockPayment",
time: "2017-06-01T00:00:00Z"
};
document.getElementById("mock_payment_button").addEventListener('click', function () {
BitcoinExpress.Wallet.PaymentRequest(paymentDetails).then(function(container) {
window.location.replace(container.PaymentAck.return_url);
}).catch(function(err) {
console.log("PaymentRequest error returned ", err);
});
});


Members
-
<private> _playerService :PlayerClient.PlayerService
-
Player service instance
Type:
- PlayerClient.PlayerService
-
activeXWindowProperty :string
-
Name of the ActiveX object property
Type:
- string
-
autoplay :boolean
-
autoplay ON|OFF
Type:
- boolean
-
flashConfiguration :PlayerClient.Config.PlayersConfiguration.FlashConfiguration
-
Data object for Flash Player
Type:
-
flashPlugin :string
-
path to flash player plugin
Type:
- string
-
hlsPlugin :string
-
path to HLS player plugin
Type:
- string
-
id :string|undefined
-
DOM element id. Optional property.
Type:
- string | undefined
-
logger :PlayerClient.Config.Logger
-
Custom logger
Type:
-
mediaType :PlayerClient.Constants.MEDIA_TYPE
-
Bitmask of media types supported by the program.
Type:
-
playersConfiguration :string
-
path to JSON configuration file
Type:
- string
See:
-
- JSON file format PlayerClient.Config.PlayersConfiguration.PlayersConfigData
-
playersOrder :array
-
List of media players in the preferred order.
Type:
- array
-
silverlightConfiguration :PlayerClient.Config.PlayersConfiguration.SilverlightConfiguration
-
Data object for Flash Player
Type:
-
silverlightPlugin :string
-
path to Silverlight player plugin. This relative path is based on the location of the HTML page that will contain the object element.
Type:
- string
-
streams :PlayerClient.PlayerParams.Streams
-
A collection of URLs for the media
Type:
-
thumbnail :string|undefined
-
Program's thumbnail. Optional property.
Type:
- string | undefined
-
wmpConfiguration :PlayerClient.Config.PlayersConfiguration.WMPConfiguration
-
Data object for Windows Media Player
Type:


general
fortify health & restore health
blue mountain flower + wheat
fortify health & restore health & restore stamina
bear claws + charred skeever hide + wheat
regenerate health & regenerate magicka
garlic + namira's rot + salt pile
or dwarven oil + garlic + juniper berries
resist fire & resist frost & resist shock
fly amantia + hawk beak + snowberries
resist fire & resist frost & resist poison
mudcrab chitin + snowberries + thistle branch
cure disease & restore health & restore stamina
charred skeever hide + eye of sabre cat + hawk feathers
cure disease & restore health & restore stamina & resist poison
charred skeever hide + eye of sabre cat + mudcrab chitin
regenerate health & invisibility
luna moth wing + vampire dust
resist magic & invisibility
luna moth wing + nirnroot + tundra cotton
mages
fortify magicka & regenerate magicka & restore magicka
jazbay grapes + moon sugar + red mountain flower
fortify magicka & restore magicka
briar heart + red mountain flower
or creep cluster + red mountain flower + tundra cotton
archers
fortify marksman
any of: canis root, elves ear, juniper berries, spider egg
warriors
fortify block & fortify health & restore stamina
bear claws + boar tusk + honeycomb
or bear claws + boar tusk + pearl
thieves
fortify pickpocket
any of: blue dartwing, nordic barnacle, orange dartwing, slaughterfish egg
fortify lockpicking
any of: ashen grass pod, falmer ear, namira's rot, pine thrush egg, spider egg
fortify one-handed & fortify sneak & resist frost & restore stamina
hawk feathers + purple mountain flower + small pearl
fortify light armor & fortify one-handed & fortify sneak
beehive husk + hawk feathers +
any of: bear claws, canis root, hanging moss, rock warbler egg, small pearl
fortify destruction & fortify sneak & restore magicka
beehive husk + ectoplasm + human flesh
fortify sneak & resist frost & restore stamina
frost miriam + purple mountain flower + silverside perch
poisons
damage health & ravage health & weakness to poison
deathbell + giant lichen + skeever tail
damage health & ravage health
crimson nirnroot + giant lichen + skeever tail
damage health & lingering damage health
crimson nirnroot + imp stool + mora tapinella
or imp stool + orange dartwing + river betty
damage health & lingering damage health & paralyze
human flesh + imp stool + slaughterfish egg
or human flesh + imp stool + scrathecraw
damage health & slow
deathbell + river betty + salt pile
damage health & slow & weakness to poison
deathbell + pine thrush egg + river betty
lingering damage health & ravage health & damage health
imp stool + scathecraw + skeever tail
lingering damage health & paralyze
canis root + imp stool +
any of: orange dartwing, mora tapinella, scathecraw


Just a simple element to wrap some JSON and provide it via getData() method.
getData()
This is mainly used to mockup some data from the server.


Grand Master Tobias:
What's this? The Sealed Prophecy - Path of the God? Surely you must have been sent by Shadow Fox!
To discover the location of the angel, we must open the seal.
Wait a moment while I do so...
Once this document is unsealed, I must ask a favor of you.
Wait.


Ergonomics is the process by which the Java Virtual Machine (JVM) and garbage collection tuning, such as behavior-based tuning, improve application performance. The JVM provides platform-dependent default selections for the garbage collector, heap size, and runtime compiler. These selections match the needs of different types of applications while requiring less command-line tuning. In addition, behavior-based tuning dynamically tunes the sizes of the heap to meet a specified behavior of the application.
This section describes these default selections and behavior-based tuning. Use these defaults first before using the more detailed controls described in subsequent sections.
A class of machine referred to as a server-class machine has been defined as a machine with the following:
2 or more physical processors
2 or more GB of physical memory
On server-class machines, the following are selected by default:
Throughput garbage collector
Initial heap size of 1/64 of physical memory up to 1 GB
Maximum heap size of 1/4 of physical memory up to 1 GB
Server runtime compiler
For initial heap and maximum heap sizes for 64-bit systems, see the section Default Heap Size in The Parallel Collector.
The definition of a server-class machine applies to all platforms with the exception of 32-bit platforms running a version of the Windows operating system. Table 2-1, "Default Runtime Compiler", shows the choices made for the runtime compiler for different platforms.
Table 2-1 Default Runtime Compiler
| Platform | Operating System | DefaultFoot1 | Default if Server-ClassFootref1 |
|---|---|---|---|
|
i586 |
Linux |
Client |
Server |
|
i586 |
Windows |
Client |
ClientFoot2 |
|
SPARC (64-bit) |
Solaris |
Server |
ServerFoot3 |
|
AMD (64-bit) |
Linux |
Server |
ServerFootref3 |
|
AMD (64-bit) |
Windows |
Server |
ServerFootref3 |
Footnote1Client means the client runtime compiler is used. Server means the server runtime compiler is used.
Footnote2The policy was chosen to use the client runtime compiler even on a server class machine. This choice was made because historically client applications (for example, interactive applications) were run more often on this combination of platform and operating system.
Footnote3Only the server runtime compiler is supported.
For the parallel collector, Java SE provides two garbage collection tuning parameters that are based on achieving a specified behavior of the application: maximum pause time goal and application throughput goal; see the section The Parallel Collector. (These two options are not available in the other collectors.) Note that these behaviors cannot always be met. The application requires a heap large enough to at least hold all of the live data. In addition, a minimum heap size may preclude reaching these desired goals.
The pause time is the duration during which the garbage collector stops the application and recovers space that is no longer in use. The intent of the maximum pause time goal is to limit the longest of these pauses. An average time for pauses and a variance on that average is maintained by the garbage collector. The average is taken from the start of the execution but is weighted so that more recent pauses count more heavily. If the average plus the variance of the pause times is greater than the maximum pause time goal, then the garbage collector considers that the goal is not being met.
The maximum pause time goal is specified with the command-line option -XX:MaxGCPauseMillis=
<nnn>
. This is interpreted as a hint to the garbage collector that pause times of <nnn>
milliseconds or less are desired.  By default there is no maximum pause time goal. These adjustments may cause garbage collector to occur more frequently, reducing the overall throughput of the application. The garbage collector tries to meet any pause time goal before the throughput goal. In some cases, though, the desired pause time goal cannot be met.
The throughput goal is measured in terms of the time spent collecting garbage and the time spent outside of garbage collection (referred to as application time). The goal is specified by the command-line option -XX:GCTimeRatio=
<nnn>
. The ratio of garbage collection time to application time is 1 / (1 + <nnn>
). For example, -XX:GCTimeRatio=19
sets a goal of 1/20th or 5% of the total time for garbage collection.
The time spent in garbage collection is the total time for both the young generation and old generation collections combined. If the throughput goal is not being met, then the sizes of the generations are increased in an effort to increase the time that the application can run between collections.
Do not choose a maximum value for the heap unless you know that you need a heap greater than the default maximum heap size. Choose a throughput goal that is sufficient for your application.
The heap will grow or shrink to a size that will support the chosen throughput goal. A change in the application's behavior can cause the heap to grow or shrink. For example, if the application starts allocating at a higher rate, the heap will grow to maintain the same throughput.
If the heap grows to its maximum size and the throughput goal is not being met, the maximum heap size is too small for the throughput goal. Set the maximum heap size to a value that is close to the total physical memory on the platform but which does not cause swapping of the application. Execute the application again. If the throughput goal is still not met, then the goal for the application time is too high for the available memory on the platform.
If the throughput goal can be met, but there are pauses that are too long, then select a maximum pause time goal. Choosing a maximum pause time goal may mean that your throughput goal will not be met, so choose values that are an acceptable compromise for the application.
It is typical that the size of the heap will oscillate as the garbage collector tries to satisfy competing goals. This is true even if the application has reached a steady state. The pressure to achieve a throughput goal (which may require a larger heap) competes with the goals for a maximum pause time and a minimum footprint (which both may require a small heap).


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Abstact
There exist a substantial amount of residents living in Toronto’s apartment buildings. In this paper we explore the Apartment Building Evaluation dataset, which was a survey conducted by OPENDATA Toronto. In this project, we focus on three important basics of the apartments’ condition which are: the security, lobby condition and parking area condition. And the result shows that majority of the residents are satisfied with the security yet the parking condition still needs to be improved.
Introduction
Since Toronto is one of the biggest and most wealthy cities in Canada, the existence of huge population makes apartment buildings absolutely necessary to this city. Millions of people are living in Toronto’s apartment buildings. This leads to a interesting question: are they really enjoying their stay? On which parts so far are Toronto’s apartments doing a great job and which parts are still needed to be improved? Base on the data provided by Opendata Toronto, this project will deeply analyze the real need of Toronto’s apartment residents.
The dataset contains building evaluation scores for all evaluated buildings that are registered in the Apartment Building Standards(ABS) program. All areas are reviewed for each building with rates assigned by scores from 1 to 5, with 1 being the worst condition and 5 being the best condition. The overall scores are rated out of 100. However, we transform the overall scores into out of 5 to get a clearer view on the data.
Part1: Overview on the data.
summary(na.omit(score_five))
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 1.850 3.500 3.800 3.796 4.100 5.000
par(mfrow = c(2,2))
hist(na.omit(score_five), main="Histogram of Overall Score")
hist(as.numeric(SECURITY), main="Histogram of Security")
hist(as.numeric(ENTRANCE_LOBBY), main="Histogram of Lobby")
hist(as.numeric(PARKING_AREA), main="Histogram of Parking")
The average overall score of Toronto apartments is 3.796/5, with the lowest score of 1.85 and the highest score of 5. And half of the apartments are between the score range of 3.5~4.1. From the histogram of overall score, we see the graph is slighly left-skewed, and the score gathers around 3.75.
Moving onto the other three histogram. The histogram of security is extremely left-skewed, which shows that most of the buildings have a well provided security. The histogram of lobby indicates that most of the residents think their lobby condition is 4 out of 5. However, the histogram of parking condition shows that residents are not very satisfied with the parking condition of the apartments.
Part2: How are the rating influence the overall score.
par(mfrow = c(1,3))
plot(SECURITY, score_five)
plot(ENTRANCE_LOBBY, score_five)
plot(PARKING_AREA, score_five)
From the plots above, we find a positive linear relationship between the overall score and each condition score. As the rating on security, lobby and parking goes higher, the overall score of the building increases simultaneously. This implies that all three conditions are important elements that residents care about the buildings.
Part3: Concluding the quality of Toronto apartments.
element <- c("Overall Score", "Security", "Lobby", "Parking")
boxplot(score_five, as.numeric(SECURITY), as.numeric(ENTRANCE_LOBBY), as.numeric(PARKING_AREA), names = element, horizontal = FALSE, main = "Boxplot of Overall Score and Area Conditions", ylab= "score out of 5")
The boxplots above further states the residents’ rating on each area condition. The dots on the plots are outliers which are ignored in our study. We should be proud of the security service of Toronto apartments since most of the residents give high scores on it. The condition of lobby is also outstanding with the proofs from the majority. However, the average score of 3 out of 5 of parking condition should be an alert to all the building management.
Weakness and Next-step
The dataset was detailed and useful. However, there are more possible elements that are influcing the residents’ living condition. For example, the service from building managment, the amount and quality of amenity provided, the nearby community services and so on. There also exist a lack on parking condition rating. For example, some buildings do not have large parking space, but there might be a parking area nearby the building which is also convinent to the residents.
To improve the survey, we should gather opinions from the residents and analyze what are their real needs beside the ones they are rating in this survey.
Conclusion:
Residents in Toronto apartments are living in a safe and clean environment with high-level security service and well rated lobby area. Yet they are not very satisfied with the parking condition provided by the building.
Reference
Wickham et al. (2019)
Allaire et al. (2020)
Open Data Dataset. (n.d.). Retrieved September 27, 2020, from https://open.toronto.ca/dataset/apartment-building-evaluation/
Allaire, JJ, Yihui Xie, Jonathan McPherson, Javier Luraschi, Kevin Ushey, Aron Atkins, Hadley Wickham, Joe Cheng, Winston Chang, and Richard Iannone. 2020. Rmarkdown: Dynamic Documents for R. https://github.com/rstudio/rmarkdown.
Wickham, Hadley, Mara Averick, Jennifer Bryan, Winston Chang, Lucy D’Agostino McGowan, Romain François, Garrett Grolemund, et al. 2019. “Welcome to the tidyverse.” Journal of Open Source Software 4 (43): 1686. https://doi.org/10.21105/joss.01686.


Travelling is a good way to release stress. Go out and see the world with us! Cant wait to see you. “The world is a book, and those who do not travel read only a page.” During travelling you will meet people that are very different from you. You will learn to accept and appreciate these differences. Traveling makes you more open and accepting.
Travelling is a good way to release stress. Go out and see the world with us! Cant wait to see you. TTravelling can teach you more than any university course. You learn about the culture of the country you visit. If you talk to locals, you will likely learn about their thinking, habits, traditions and history as well!
Turkey has so many magical spots the world doesn’t know about. The balloons in Cappadocia, Paragliding at the turquoise coast in Fethiye or the salt pools in Pamukkale. Turkey is a must visit!
Far and away the most popular time to visit is April, which is cherry blossom season. And Autumn (September – November) is good for the fall foliage. The summer is hot and humid, and often rainy up until early July!
A stunning view on HuangShan will amaze you.
Summer in Bali.
A beautiful autumn in Canada.
Have a nice holiday in Iceland.


Posted by: Tosca Wilson
Date: 24.08.2019
So far my goal is to successfully complete this course, and then gain employment as a junior developer to further hone my skills. Other than that, I can't say that I have a firm career pathway in mind, as I feel that I do not yet know enough about the industry to decide on this yet. I think that one day I would like to take my skills and work somewhere overseas. Another thing I would like to consider as a goal would be the ability to work flexibly and remotely. I do know that some companies would offer these types of working conditions, or this could also be achieved by working for myself.
I really enjoy problem solving and developing ideas. Anytime I am faced with a problem, I turn it over in my head to solve it before I take action. With regards to my limitations, something that I struggle with is putting my thoughts into words, especially when I am put on the spot and asked to express my ideas. This can sometimes mean that I miss the opportunity to share my thoughts.
While at EDA, I would like to develop stronger communication skills. More specifically, I would like to become more confident and articulate when communicating my thoughts and ideas with others.
My strengths should especially help when it comes to problem solving. When I come across a problem in my learning journey, I will spend time to turn it over in my head to come up with a solution. It can sometimes be uncomfortable to not know what to do, but I will remind myself that discomfort is a good indication that you are about to learn something new.
When I am faced with a problem that I am unable to solve on my own, I am committed to consulting with my cohort, and if necessary also with a facilitator. Although I am very much inclined to try and solve a problem on my own, I understand that sometimes it can be a more efficient and effective learning approach to ask for help from others. From the facilitation team, it would be very valuable for a relationship to be established where as a student I feel comfortable to ask for support whenever it might be needed, and to also receive constructive feedback when necessary.
During September I will be away in Japan for 2 weeks on holiday. This time away will be for the entirety of Sprint 4 of Foundations. My plan is to get as far through Sprint 4 as I can before I leave, and to continue working on it as much as I can while away. When I return from my holiday, ideally I would have finished Sprint 4 and be starting on Sprint 5. Should this not go to plan, I have an entire week free from work and any other commitments right before Bootcamp begins and can use this time to catch up.


This challenge is organised by @anomadsoul and it’s a fun one! Please take a look at his original post if you want to join this challenge too!
I joined Steemit in May 2017 and I have been an active member here for almost one year and a half now. As an olde user, I am happy to know that Eric launched the challenge and gives us all an opportunity to let other Steemians to know more about us by selecting 10 posts that we want everyone to read.
Introduce Myself Post
The first post I would like to share is my “Introduce Yourself” post. At that time, I had already been on the platform for some days, and finally I decided to show my face and verification photo. Hope this can help newcomers to know more about my personal life.
Travel with Me to the USA
Back then, we wrote posts of different topics hoping to get the Chinese whale @abit’s upvote. This was my first travel series and it was posted by @someone, a project which helped promoting the good content in the Chinese community.
1st Steemit Team HK gathering
This is the first Steemit Team HK gathering and after that three of us were lucky to receive @ned’s SP delegation to help building up the Hong Kong and Chinese community.
Anime Drawing Challenge
It was the first drawing challenge I have organised and I was so surprised by the quality of the entries. Hundreds of entries were received and many of them are with very good quality.
Suggestions to the newbies
This post was a summary of some useful tips I gave to the newbies in the #cn community. Personally I think many of them are very useful. Hope that this article could help the newbies.
Design your own Steemit hero!
This was the second drawing challenge I have organised and this time the theme was Steem hero. Look at the entries and see how creative the participants were!
Steemit Guangzhou Meetup
Here comes the Steemit Guangzhou Meetup. Finally we were able to meet other Steemians in the #cn community in person. @rivalhw was the organiser of the meetup and he spent a lot of effort. He even made souvenirs with the new Steemit logo and sent them as a gift to us.
Rep 70! My Steemit Milestone!
This post was about me reaching my Steemit milestone. I finally reached Rep 70 and decided to share my joy with my followers!
Let’s show our Steem SpiritBasically it was a post about what I have done so far to promote Steem and how they demonstrate Steem spirit!
Project #cn-curationOf course I have to mention my project #cn-curation. This project aims to discover the quality content in the #cn community and give them more rewards. @cnbuddy and @team-cn have helped a lot to make it happen and we have upvoted hundreds of posts with good quality so far. We now reached Volume #51
Once again, thanks @anomadsoul for organising this awesome challenge and let my new followers to know more about me.
Now I would love to nominate @aaronli, @susanlo and @honoru to participate in this challenge.
This page is synchronized from the post: ‘Get To Know Me Challenge - my entry’


--- layout: post title: "網站升級: CommunityServer 2007.1" categories: tags: ["Community Server","技術隨筆","有的沒的","水電工"] published: true comments: true permalink: "/2007/11/12/網站升級-communityserver-2007-1/" redirect_from: - /columns/post/2007/11/12/e7b6b2e7ab99e58d87e7b49a-CommunityServer-20071.aspx/ - /post/2007/11/12/e7b6b2e7ab99e58d87e7b49a-CommunityServer-20071.aspx/ - /post/e7b6b2e7ab99e58d87e7b49a-CommunityServer-20071.aspx/ - /columns/2007/11/12/e7b6b2e7ab99e58d87e7b49a-CommunityServer-20071.aspx/ - /columns/e7b6b2e7ab99e58d87e7b49a-CommunityServer-20071.aspx/ - /blogs/chicken/archive/2007/11/12/2806.aspx/ wordpress_postid: 135 ---
周日下午趁小孩都回外婆家, 花了點時間把家裡該裝的裝一裝, 該接的接一接, 還有一點空檔, 就把拖了很久的網站升級處理一下... 原本的版本是 CS 2007 (3.0), 中間推出了 3.0 SP1, SP2, SP3 beta 都跳過去沒理它, 這次 2007.1 (3.1) 出來手又癢了起來...
過程就沒啥好說了, 失敗了好幾次, 最後決定整個重裝... 抓了 2007.1 的官方版本, 把舊的 db 配上它的 upgrade script 執行完後掛上去, 基本功能就會動了, 最後再把 ~/blogs, ~/photos, ~/forums 等有 storage 的目錄搬過去, 再把我自己客制過的 themes 重改一次 ( my god, themes 裡的檔案全都調過, 原本的 themes 蓋過來可以跑, 不過心裡毛毛的 )... 總算大功告成. 事後順手也把同一台 server 另外兩套 CS 也順便升級了一下.
老實說我也沒很注意 2007.1 到底改了啥, 就貼一下吧, 搞不好大家之前碰到的鳥問題已經被解決掉了... 正好鴕鳥混過去, 哈哈 [H]
以下是 CS2007.1 release notes:
Below are changes available in Community Server 2007.1
-------------------------------------------------------------------
Enhancements
- Updated caching framework, performance updates, added locking support for several of the application-wide collections
- SQL performance updates and best-practices updates
- Added CreateEditWeblogPostForm, DeleteWeblogPostForm, and associated sub-form controls from CS2008 to support creating/editing/deleting blog posts in the front UI using Chameleon.
- Updated styles on the TinyMCE wrapper's content to provide some default spacing and use a larger default font size.
- Updated TagCloud controls to support disabling the "no tags" message and "no related tags" messages. Updated all existing themes (except for tag browsing pages) to not render the "no tags" message.
- Updated SqlProviders to resolve LINQ SortOrder namespace ambiguity
- Added support for sorting and paging LinkCategory and Link objects in the API and via Chameleon.
- Added toggle button for enabling/disable application tokens
- Tweaked app tokens list a little bit to show the time for the last used column
- Added a new AdPlacementOptions to WrappedRepeater, AlternatingSeperator - places an ad after every other item starting after the first.
- Updated TinyMCE to use the latest wrapper.
- Updated the email job only retrieves as many messages as it will send from the email queue (prevent large queues from causing timeouts)
- Updated notifications and mass emails to enforce the check on a user's "Enable Email" global setting and "Allow Site to contact me" setting
- Updated email notifications to check the enable thread tracking for post replies
- Updated mass emailing to take place on a background thread
- Updated Telligent.Registration.dll to address an issue where the add-ons could get stuck if they start before SQL on a reboot/startup
- Updated Telligent.MailGateway.Common.dll to address issues with XML cleaning in the core library and downloading only as many messages as needed from the email queue
- Updated user date formats so that month-day-year is 6-1-2007 instead of 06-01-2007
- Updated Windows Live Writer support by implementing keywords for custom tags and removing excerpt support since it gets confused with text-mode.
- The error messages were updated so that the actual error message is displayed more prominently.
- Removed the AutoDeleteThreshold setting from the forum control panel since it is not implemented.
- Updated stylesheet to not underline the group expand/collapse toggle button.
- Updated version of CookComputing XML-RPC.NET library to use new .NET 2.0 optimized verison
- Updated list of default Weblog Ping URLS (removed Blo.gs and PubSub.com, added PingOMatic.com)
- Implemented TruncationEllipsisTemplate on the ObjectDataBase control to support custom markup/controls being used in the TruncationEllipsis
- Enabled adding new categories inline through Windows Live Writer
- Added rsd.ashx and wlwmanifest.ashx in web project, and added namespaces (Added support for RSD and WLWManifest).
- Updated MetaBlog to support excerpts, read-more, and post names
- Updated blog truncation to use readmore links
- Updated Metablog to default to the users current blog
- Added auto discovery for the current blogs metablog path
- Added basic site and blog theme
- Updated email templates for forum and forum thread emails to remove the background grey color.
- CSContext.User is only overridden with TokenUser when told via AllowTokenRequests(bool requirePrivateToken)
- Added rendering of news to the "Traveler" blog theme's sidebar.
- Added support for TemporaryUserTokens that expire after 3 hours
- Change password now uses a temporary user token
- Added support for disabling exception logging. It is disabled by default.
- Moved keep-alive code from global.js into the KeepAlive control. Updated Editor control to *always* render a KeepAlive control. Deleted web/utility/keepalive.aspx
- Added a few performance improvements to ThreadQueryBuilder classes: Only joining to cs_threads if we really have to, Adding a cs_Sections.ApplicationType filter back in
- Changed the expiration date from 30 days to 7
- Exception logging now occurs in background cache tasks
Bug Fixes:
- FileSystemWatcher pathing fix
- Request/Response encoding fix
- You can now resize the editor horizontally in the content editor modals
- You can now override an editor option without specifying type on the control
- You are no longer redirected to login when browsing a site that has forums at root while you are anonymous.
- Updated inline text editor to not overlap its popup container
- Updated Telligent.Glow.Modal to use frameborder='0' instead of frameborder='no'
- Create/Edit Blog Page Validation fixed so that appkey cannot be blank
- Added code and note bbcode and updated existing processing order of scrubbing modules
- Enabled checking of the user's Enable Email setting on a wide variety of message types
- Corrected all references in Chameleon controls to OpenWindow function in global.js to use a direct call to window.open.
- Updated Forum BreadCrumb control to use the current rewritten URL name instead of the rendered URL to determine the current page
- Updated EntryThumbnail control to render the file extension in the alt attribute.
- Updated EntryThumbnail control to render with an Image control and default to 0 border width and no alignment.
- The parent post cache is now expired properly when creating a new post in a thread. This allows a reply to post to always display in a thread after it is created.
- Create edit blog post now maintains state better
- Added validation for the user's email address to Users.Create
- Fix for Gallery search results from searchbarrel linking to image not to gallery page
- Removed the ability to rename or delete the anonymous user
- Fixed issue where GalleryService.Update failed to set the PostID, which caused it to always fail.
- Updated cs_User_Delete sproc to update author/post ID's as well as names
- Disabled subforums no longer require user to login in parent forum
- Fixed theme cache name so that the cache key is correct. Previously theme configuration were never getting retrieved from cache correctly.
- Changed create user page so that validation occurs when fields change as oppose to whenever a key was pressed.
- Group RSS Feed no longer causes Exception
- Pager added to the default aggregateentrylist control for the file gallery
- Clicking the Advanced Search link from a search results page now populates the advanced search options form for the lean and green theme as well as default
- Corrected QuickReply link to only refresh the page if false (and not undefined OR false) is passed as the callback parameter.
- Fixed EXIF page to show the full list of tags.
- Fixed photo post edit so it decodes the subject before populating the text box in the CP (to prevent double encoding)
- Fixed all auto-syndication registration to not re-html-encode section names.
- Fixed issue with users in the Member Administrators role not being able to change user passwords
- Fixed spelling error in the API... renamed User.EnableAvtar to User.EnableAvatar
- Updated default and leanandgreen themes to hide "view all users" link when "Display Member List" is set to "No" in the Control Panel.
- The SaveExtendedUserData call was moved into the event handler for the submit button, before the first call to sub-forms.
- You can now delete a tag that is disabled.
- User Points can now display without Post Points.
- Fixed issue with order of permissions not being handled properly
- Control Panel Report page title now shows correct text
- Fix for linking over to Shutterfly showing 0x0 as the picture's size.
- Fix for null reference on private messages from CS 2.x that were to users that were later deleted
- Fixed ForumSqlProvider to save sticky info on edited posts
- Corrected issue resulting in multiple encoding of the AvatarUrl property.
- Updated edit user form in the control panel to always show the user's Username in the "Alias" field.
- Updated blog admin control panel to properly decode the blog name.
- Corrected FireFox rendering issue on user+avatar lists in the default and lean and green themes.
- Fixed issue where Weblog XML-RPC pings do not get sent in some scenarios.
- Corrected misplaced </div> tag issue in PoisonIvy, Gertrude, Luxinterior, and Photos blog themes causing nested comments.
- Changed Roller Blog add-feed sproc to set Last Modified to current time - interval, so that the feed gets pulled the next time the job runs after the feed is added.
- Corrected rendering issue in the Control Panel in FireFox prior to JavaScript loading
- Updated the HTMLScrubber regex to use slightly different syntax which prevents infinite loop issue in FireFox.
- Corrected invalid anchor tag in blog themes.
- Added check for cs_Posts.IsIndexed in all SearchBarrel-generated queries.
- Fixed failed check to see if the user was anonymous within MailGateway
- Fixed how SPAM blocker counts links
- Fixed an issue with a missing resource label
- Updated CallbackPager to always render the PagedContent contents.
- Fixed issue with deserialization returning as successful when the output object is null
- Blog pages now show up in the tag post list if set to be aggregated, and the aggregate options are visible when creating a new page.
- Corrected thread view count to register one view per thread per rendered page regardless of the number of posts displayed on the page.
- Removed script to enable/disable "Join" button on the registration form in the default and lean-and-green themes to prevent issues with auto-complete.
- Updated TinyMCE wrapper to set the document_base_url TinyMCE option to the parent window's URL when the editor is opened in a Modal.
- Fixed notifications of message being flagged for moderation by MailGateway being queued with SettingsID of 0
- License usage colors are now cleared after uploading a license.
- Updated truncation ellipsis markup to render within the content wrapper (link) on ObjectDataBase control.
- Corrected next/previous thread links to direct to the thread's URL.
- Updated UserAvatarSubForm to set the remote avatar URL (if available) when an avatar is uploaded.
- cs_system_GenerateWeblogYearMonthDayList and cs_vw_weblog_PostByYearMonth now has some sql included to attempt to build the roll-up tables.
- Fixed regression from Bug Fix #1391 with AppKey being a required field on the blog creation page
- Selecting 'Hide Topics I've Read' in the forum filtered thread control now keeps the unread announcements visible on the first page
- You can now delete a forum post without it sending email
- Tweaks to cs_weblog_Post_Create and cs_weblog_Post_Update to ensure that UserTime was never NULL.
- Corrected potential XSS issue in User RSS Feeds
- Added EnsureHtmlEncoded calls to loaded TemporaryRssFeeds and TemporaryRssFeedItems content.
- Updated UserSearchForm to redirect to the rewritable URL instead of directly into the current theme.
- Pager fixed in the manage photo comments page so that you can page past the first 2 pages.
- Membership.GetRoles result set creation updated to ensure roles and role icons are re-populated after cache expiration
- Updated default Regex validation patterns for user names and passwords and ensured that these patterns always match the entire string when set.
- Updated sql to only change the regex pattern if the pattern [a-zA-Z]+[^\<\>]* was in the UsernameRegex before
- Added tabindex="-1" to all TinyMCE buttons to prevent tab-stops when navigating into the editor using the keyboard.
- Added validation of RSS feed URLs and external avatar URLs to ensure they are HTTP-based.
- Updated SearchBarrel to require Read access from applications supporting Read permissions.
- Adding ']' to a post no longer causes the post to pass the duplicate post check.
- Disabling post emoticons now hides the emoticon radio button list from the Forum options tab
- File Gallery comment URL's now work correctly, displaying the entry they belong to
- Corrected issue preventing section filters from being saved.
- Updated the form adapter to only update the form's action attribute when the page's URL has been rewritten by CS to ensure compatibility with external, non-rewritten pages within CS.
- Updated the thread queries used by blog and file gallery search indexing to specify IgnorePermissions=true so that all blogs and file gallery posts are indexed.
- Corrected infinite redirect issue when an invalid character exists in the URL.
- Changed const string cacheKey = "UserLookupTable" to include SettingsID
- Photo Gallery now supports HTMLEncoding a submitted user name field
- Added ApplicationName to the UserRoleNames cache key
- Corrected page height issue in IE when using tabbed panes.


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PM Imran to launch Clean Green Pakistan Index | Pakistan - Geo.tv
by Web DeskPrime Minister Imran Khan will on Monday launch the first ever barometer in Pakistan capable of measuring green character and cleanliness of cities, reports Radio Pakistan.
The barometer, called Clean Green Pakistan Index, aims at improving overall green and clean outlook of cities. Talking to media in Islamabad, Advisor on Climate Change Malik Amin Aslam says the launch will kick off competition on various indicators.
He said at the grand launching ceremony, the Prime Minister would also announce the start of the first phase of a six-month competition among 19 cities of Punjab and Khyber-Pakhtunkhwa.
Amin Aslam said the CGPI has been rolled out under the Prime Minister Imran Khan's political manifesto of clean and green Pakistan and environmental conservation and sustainability.


What is it good for?
The systems development life cycle (SDLC), also referred to as the application development life-cycle, is a term used in systems engineering, information systems and software engineering to describe a process for planning, creating, testing, and deploying an information system. The systems development life-cycle concept applies to a range of hardware and software configurations, as a system can be composed of hardware only, software only, or a combination of both.
"Systems Development Life Cycle" Wikipedia. Wikimedia Foundation [1]-
Discover
Research and determine the project's current situation and needs.
-
Define
Establish the scope of the project, planning, and project methodologies.
-
Design
Design using the Style Guide and other approved brand identity assets. Technical and functional design decisions are made in this stage.
-
Develop
Coding. Test it and repeat until development sins can be forgiven. Write Documentation.
-
Deploy
Deployment runs concurrently with Development.
-
Repeat - Iterate - Improve


(271 entries)
Comparative evolution: Is the data informative? 31 Dec 2010
Stochastic limits to evolutionary branching 30 Dec 2010
Open Notebook Science Abstract 30 Dec 2010
adaptive-dynamics Simulations 29 Dec 2010
DoE renewal and a year in review 24 Dec 2010
Writing, Cloud Computing, and #scio11 23 Dec 2010
Sun: Visualizing my coding over the past year 20 Dec 2010
Thurs: writing section on comparing to AIC 16 Dec 2010
Weds: Example sets & more EC2 15 Dec 2010
Tues: evolution thoughts while writing... 14 Dec 2010
Back to Writing 13 Dec 2010
Citations 11 Dec 2010
Warning signals manuscript 10 Dec 2010
Exploring Power in Warning Signals 09 Dec 2010
Practice SICB Presentation 08 Dec 2010
Identifying Warning Signals 04 Dec 2010
CPB : David Collar 01 Dec 2010
Further treatment of the limiting models 29 Nov 2010
Challenges in estimating phylogenetic signal 29 Nov 2010
Likelihoods for quadratic models cont 28 Nov 2010
Implementing Likelihoods for quadratic models 27 Nov 2010
Tweets from an Ecology Field class 25 Nov 2010
Warning signals: Likelihoods Straight-up 24 Nov 2010
Power in simple tests 22 Nov 2010
Two questions 21 Nov 2010
Making R twitter? 21 Nov 2010
Fri: extending Geiger to Monte Carlo method 19 Nov 2010
Thurs: evolution likelihood 18 Nov 2010
Weds 18 Nov 2010
Tues seminar 16 Nov 2010
evolution today: Discussion groups, writing, etc 15 Nov 2010
evolution statistics 11 Nov 2010
Tuesday - SDEs then back to phylogenetics 10 Nov 2010
Monday and some phylogenetics 08 Nov 2010
Welcome to my Lab Notebook 08 Nov 2010
Friday: Evolution reading, writing 05 Nov 2010
Thursday 05 Nov 2010
Reviews, organization, rewrites 03 Nov 2010
A new twist on the approach 28 Oct 2010
Red Noise (aside exercise) 28 Oct 2010
Warning Signals -- Where are we now? 27 Oct 2010
Correcting for the mean dynamics 26 Oct 2010
Warning Signals 2 21 Oct 2010
Spatial Warning Signals, power, etc 21 Oct 2010
ecology Abstract 20 Oct 2010
Adaptive Dynamics Abstract 20 Oct 2010
Warning Signals 19 Oct 2010
Teaching 18 Oct 2010
Status update 15 Oct 2010
Writing continues 14 Oct 2010
Wednesday 13 Oct 2010
a day of writing 12 Oct 2010
Still writing 11 Oct 2010
LR Manuscript 05 Oct 2010
Monday 04 Oct 2010
Likelihood Ratio Paper 03 Oct 2010
Thursday 30 Sep 2010
Adaptive Dynamics Updates 30 Sep 2010
Writing 15 Sep 2010
Writing 14 Sep 2010
Power plots 14 Sep 2010
Peter meeting 13 Sep 2010
Meeting with Alan 10 Sep 2010
Lab Notebooks 07 Sep 2010
Meeting with Sam 07 Sep 2010
evolution Research Abstract 04 Sep 2010
Entry title 01 Sep 2010
Tuesday 31 Aug 2010
Summer Review 30 Aug 2010
Adaptive Dynamics 30 Aug 2010
Likelihood ratio ToDo 27 Aug 2010
Likelihood Ratio Paper- Power in Trees 26 Aug 2010
Likelihood Ratio Manuscript 25 Aug 2010
Writing 19 Aug 2010
Entry title 19 Aug 2010
Warning Signals -- still in code development 18 Aug 2010
Warning Signals 17 Aug 2010
Warning Signals 16 Aug 2010
Warning Signals 15 Aug 2010
Adaptive Dynamics 13 Aug 2010
Warning Signals 12 Aug 2010
Adaptive Dynamics 12 Aug 2010
Adaptive Dynamics 11 Aug 2010
Warning Signals 10 Aug 2010
Likelihood ratio update 10 Aug 2010
Warning Signals by model choice 09 Aug 2010
Warning Signals 08 Aug 2010
Reading 07 Aug 2010
Batch Data 05 Aug 2010
Data Format functions 04 Aug 2010
Writing 03 Aug 2010
Open Science Summit Day 3 31 Jul 2010
Open Science Summit day 2 30 Jul 2010
Open Science Summit 29 Jul 2010
Cetartiodactyle data 28 Jul 2010
Parameter Estimates for Labrid-Parrotfish model 27 Jul 2010
Parrotfish Model choice 26 Jul 2010
Writing 23 Jul 2010
Writing 22 Jul 2010
Writing 21 Jul 2010
Writing 20 Jul 2010
Wainwright Meeting 19 Jul 2010
Parrotfish-Wrasse example 15 Jul 2010
Organizing analyses, data, codes 14 Jul 2010
Bootstrapping the independent alpha-sigma models 13 Jul 2010
Multivariate normal random variables 12 Jul 2010
Status - Thoughts 09 Jul 2010
Evolutionary Regime Shift examples 08 Jul 2010
Multitype OU process interfaces 07 Jul 2010
Ensemble simulations of beetle dynamics 07 Jul 2010
iEvoBio day two 30 Jun 2010
iEvoBio day one 29 Jun 2010
Evolution 2010 Day 3 28 Jun 2010
Evolution 2010 Day 2 27 Jun 2010
Evolution 2010 26 Jun 2010
CSGF Conference Thursday 24 Jun 2010
CSGF Conference Day 2 23 Jun 2010
CSGF Conference- Tuesday 22 Jun 2010
CSGF Conference- HPC Workshop 21 Jun 2010
Wainwright Lab Meeting 16 Jun 2010
Questions 10 Jun 2010
Graham & Peter Meeting 09 Jun 2010
Making slides for Evolution meeting 08 Jun 2010
Implementing the new approach 06 Jun 2010
Likelihood Calculation 05 Jun 2010
Comparative Phylogenetics Talk 04 Jun 2010
Entry title 03 Jun 2010
Actually starting at Arkin Lab 02 Jun 2010
Gamma Waiting times on individual level 01 Jun 2010
CSGF Survey 31 May 2010
Conference call w- Bob and Brett 28 May 2010
Summary of Structured Population noise so far 27 May 2010
Rethinking Beetles Noise 26 May 2010
Bug fixed! 25 May 2010
Status on Structured Populations 24 May 2010
Puzzled over the two-step jump process results 21 May 2010
Beetle dynamics exploration & adjustments 20 May 2010
Noisy Beetles 19 May 2010
Noisy beetles 18 May 2010
Annual Progress Report 17 May 2010
General matrix form and correcting equations 16 May 2010
Large Intrinsic Noise 15 May 2010
Structured Population Dynamics 14 May 2010
Beetles workshop Day 2 13 May 2010
Adaptive Dynamics 13 May 2010
Roi and Sam Comparative Phylogenetics R Workshop 12 May 2010
Hastings Beetle Workshop 12 May 2010
Peter Meeting 11 May 2010
Demographic Noise 11 May 2010
Alan Meeting 10 May 2010
Warning Signals with SDEs 09 May 2010
Likelihood calculation 07 May 2010
Goals 06 May 2010
Wednesday 05 May 2010
Primates 05 May 2010
Alan Meeting 04 May 2010
Adaptive Dynamics 04 May 2010
Adaptive Dynamics 03 May 2010
Phase1 01 May 2010
Coexistence Of The Early Dimorphism 01 May 2010
Adaptive Dynamics 30 Apr 2010
Adaptive Dynamics 29 Apr 2010
Meetings 28 Apr 2010
iEvoBio lightning talk 27 Apr 2010
Teaching 26 Apr 2010
Adaptive Dynamics 26 Apr 2010
Adaptive Dynamics 23 Apr 2010
Adaptive Dynamics 22 Apr 2010
Adaptive Dynamics 21 Apr 2010
Waiting Time 20 Apr 2010
R-sig-phylo 20 Apr 2010
Alan Meeting 20 Apr 2010
Research 19 Apr 2010
MATICCE 18 Apr 2010
iEvoBio Submission 16 Apr 2010
Branching Paper 15 Apr 2010
Wednesday 14 Apr 2010
Tuesday 13 Apr 2010
Teaching 13 Apr 2010
Teaching 12 Apr 2010
Primate chronogram 12 Apr 2010
Effective warning signals 11 Apr 2010
Research 09 Apr 2010
Research 08 Apr 2010
Comparative Phylogenetics Notebook 08 Apr 2010
Research 07 Apr 2010
Towards a meaningful warning signal metric 06 Apr 2010
Research 06 Apr 2010
Research 05 Apr 2010
Research 04 Apr 2010
Warning Signals Research 03 Apr 2010
Warning Signals 02 Apr 2010
Research 02 Apr 2010
Research 01 Apr 2010
Research 31 Mar 2010
Comparative Phylogenetics Notebook 31 Mar 2010
Research 30 Mar 2010
Still puzzling on LR 26 Mar 2010
Research 25 Mar 2010
Entry title 25 Mar 2010
Parallel R 24 Mar 2010
Bootstrapping Likelihood ratios 23 Mar 2010
Phylogenetic Tree formats 22 Mar 2010
Research 20 Mar 2010
Research 19 Mar 2010
Research 18 Mar 2010
Research 17 Mar 2010
Graham & Peter Meeting 16 Mar 2010
Computing 15 Mar 2010
Post-Workshop 14 Mar 2010
Bodega Workshop Presentations 12 Mar 2010
Phylogenetics Workshop Day 5 11 Mar 2010
Bodega Workshop Day 4 10 Mar 2010
Bodega Phylogenetics Workshop Day 3 09 Mar 2010
Bodega Phylogenetics Workshop Day 2 08 Mar 2010
Bodega Phylogenetics Workshop Day 1 07 Mar 2010
Meeting 05 Mar 2010
Friday 05 Mar 2010
Big Picture Comparative Phylogenetics 04 Mar 2010
Solution to the strange behavior in ouch 03 Mar 2010
Power in trees 02 Mar 2010
Teaching 01 Mar 2010
Parallel at last 01 Mar 2010
Parallelizing Code 28 Feb 2010
Friday 26 Feb 2010
Thursday 25 Feb 2010
Derin And Alan Meeting 24 Feb 2010
Comparing to Analytic Dynamics 23 Feb 2010
Teaching 22 Feb 2010
Monday 22 Feb 2010
Teaching 19 Feb 2010
Power in trees continues 19 Feb 2010
Power in Trees 18 Feb 2010
Meeting Goals 17 Feb 2010
Hastings Meeting 17 Feb 2010
Updating manuscript 16 Feb 2010
Parametric bootstrapping 15 Feb 2010
Implementing warning signals metrics 15 Feb 2010
Speciation 14 Feb 2010
Teaching 11 Feb 2010
Meeting w- Alan 10 Feb 2010
Follow-up on Parametric Bootstrapping 10 Feb 2010
Meeting with Graham and Peter 09 Feb 2010
Code Development for Exploring Regimes Shifts 09 Feb 2010
Updates to Code 08 Feb 2010
Exploring Difficulties with Existing Methods 07 Feb 2010
Lunch with Wainwright Lab 05 Feb 2010
Teaching 04 Feb 2010
Hastings Meeting 03 Feb 2010
The Lab Notebook Goes Open 02 Feb 2010
Teaching 25 Jan 2010
Progresschallenges 18 Jan 2010
CPB thesis proposal 10 Jan 2010


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Press release
Gove: ‘More great heads and teachers controlling schools will bring better behaviour and teaching to thousands more children.’
Michael Gove, Education Secretary, today announced that 142 schools have accepted the Government’s offer to become an academy since the Academies Act became law just over a month ago. These schools have made a commitment to work with other schools and share their expertise. This is the first wave of converters in a rolling process that allows schools to convert at any stage.
The running total of schools that will become academies this academic year is 216 so far. The current breakdown is as follows:
This is record progress; it took five years for 15 city technology colleges to open, and four years for the first 27 academies to open.
Michael Gove said:
This Government believes that teachers and headteachers, not politicians and bureaucrats, should control schools and have more power over how they are run. That’s why we are spreading academy freedoms. This will give heads more power to tackle disruptive children, to protect and reward teachers better, and to give children the specialist teaching they need.
This year’s GCSE results saw academy pupils improving at nearly three times the historic rate of state school improvement.
Heads of new academies today welcomed their new freedoms:
Patricia Sowter, Head of Cuckoo Hall Primary School, Edmonton, said:
With the new academy freedoms we will continue to develop our autonomy and take the school forward in what is an area of London that faces significant challenges and disadvantage. We will now have the flexibility to adapt and extend the curriculum, target resources more effectively, deploy specialist staff and above all build sustainable capacity to ensure continued and long term outstanding educational provision, to best meet the needs of our children and wider school community.
Cuckoo Hall remains committed to supporting and working with other schools to improve children’s achievement. As an academy, Cuckoo Hall aims to build long term sustainable capacity to continue its effective work with other schools, and will seek to widen its impact on overall school improvement.
Greg Martin, Executive Head of Durand Academy, Lambeth, said:
Becoming an academy is so important for us at Durand. We are proud to deliver an outstanding education for our pupils, in an area with one of the highest levels of social deprivation in the UK. The freedom that academy status brings will allow us to deliver and develop a flexible curriculum to ensure that these children reach their full potential and achieve the very best. We look forward to using our academy freedoms to work with other schools to raise levels of attainment across the board.
David Hampson, Principal of Tollbar Business and Enterprise College, Grimbsy, said:
The benefits of becoming an academy will be enormous - less bureaucracy certainly but also more resources which we ourselves will be able to manage. We are very happy to embrace the requirement to associate ourselves with less successful schools and indeed we already have been working with a number of other schools locally and nationally, sharing our winning ways. In fact, Tollbar, as Tollbar Edge, are the sponsors of another academy which replaces a local school in special measures. We believe that we have already demonstrated our ability to run a highly successful establishment and this fantastic initiative will certainly help us to offer even more to the young people in our care.
Dr John Marincowitz Head of the Queen Elizabeth’s School, Barnet, said:
We are delighted with our new status as an academy. Greater autonomy brings significant beneficial opportunities. For example, greater freedom to decide the curriculum will enable Queen Elizabeth’s to secure a suitably academic curriculum that is geared more accurately to the needs of our pupils. Similarly, greater autonomy means we can now ensure that the resources and services we purchase are appropriate for the school and more closely aligned to the specific requirements of our pupils. We also look forward to bolstering the support we already provide to local schools as a specialist Training School and especially Northgate Hospital School with whom we have an established relationship.
Helen Hyde, Head of Watford Grammar School for Girls, Hertfordshire, and President of Foundation, Aided Schools and Academies National Association (FASNA), said:
I am very excited by the new challenges and opportunities that are created by becoming an academy. We will use the freedoms and autonomy to improve the educational provision for our students as well as form new partnerships with schools who would like to work with us both in the UK and abroad.
Total: 203
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Published: 1 September 2010