Genetic regulatory networks are complex dynamic systems, and they can describe the interaction of gene expression of living cells. When designing novel system of wanted function, the intrinsic stabilization and regulation of kinetics activity could determine the outcome of the design, which highlight the crucial role of mathematical and physical modelling. Many works have been done to analyze the behavior of synthetic oscillators. The most well-known synthetic oscillator is the repressilator, which was the first one to be achieved with experiment by Elowitz&Leibler in 2000[7]. Their realized synthetic oscillation in one cell. In 2016, Potvin-Trottier and his coworker successfully measured the repressilator functioning features in a cluster of cells[16]. However, in order to enhance the synchronization in a population of cells, in our project, we coupled quorum sensing system with repressilator to synchronize repressilators oscillation pattern. In addition, to measure the time to reach quasi-steady-state, we included the delay time τ into the equations since time delays are omnipresent in actual complex systems[5][13][15]. The equations that we use to describe this behavior of the system are ordinary differential equations (ODE) and delay differential equations (DDE). At last, the model is shown below.
ExtraFig.1 Scheme of the repressilator network coupling a quorum-sensing system. m1, m2, m3 are the promoters of LacI, TetR and CI. The parameter β and τ correspond to the notation used later. Line with bar represents inhibition. The period of oscillation is synchronized through Ai signal(N-acyl homoserine lactones).
Firstly, let’s take a look at promoter. A promoter is a region of DNA just upstream of the coding region of a gene that acts as a regulator of the gene’s expression. There are generally three types of promoters used in synthetic biology: (1) promoters that are up-regulated by transcriptional activators, as shown in (2) promoters that are down-regulated by transcriptional repressors, as shown in Fig. 1.
Fig1. Taken from [15]. Regulation of promoters through transcriptional activators and repressors. (a) Transcriptional activators initiate transcription of a gene once bound to the promoter. In the absence of a transcriptional activator the gene is silenced, or off. (b) Transcriptional repressors inhibit transcription of a gene by binding to the promoter region. The removal of the transcriptional repressor allows the promoter to become transcriptionally active.
To derive the equation for our repressilator, we need to start with the equation of single protein. If the promoter fires at a rate αu when unbound and αb when bound, then the total rate at which initiation events occur is
On the other hand, the concentration of protein won’t increase without limitation. The most ubiquitous form of protein ‘‘degradation’’ is due to cellular growth and division, i.e. the protein concentration dilutes as the total reaction volume grows despite the real situation may be more complicated. For simplicity, we assume the cells’ volume grow exponentially with a rate μ as is shown in Fig.2, then we can write
When we introduced our project, we attracted people’s attention successfully. Many people showed their interest in our project in the panel session and they also gave us some good suggestions.
But sometimes this approximation of dynamics can be poor, the general way is to include the dynamics of related mRNA. The reason is that it actually requires quite a lot of steps to produce a functional protein. Of course, we can’t write down every step’s equation. It’s hard to do that, and it takes much time for computer to numerically calculate the result. However, generally, ODE including mRNA dynamics is accurate enough for most of the situations since some reactions like oligomerization, TF binding and protein folding occur on a much faster time scale. Hence, we can write a 2-dimensional system as
As for the system of repressilator: LacI, TetR, CI, following the work of Elowitz and Leibler[7], we can naturally expand equations to 3 groups and they are coupling with each other.
Here, m1, m2, m3 are the concentrations of LacI, TetR and CI. Let αi be the maximum production rate. For simplicity, we assume those constants are the same for each protein and mRNA, i.e. α1=α2=α3; n₁=n₂=n₃; K₁=K₂=K₃; λ₁=λ₂=λ₃; αleak1=αleak2=αleak3. By now, we have got the equations to represent the repressilator system. In fact, we can rescale concentrations and time to arrive at dimensionless equations. So that time is rescaled by mRNA lifetime, the protein concentration is written in units of K, the mRNA concentration is rescaled by translation efficiency (number of proteins produced per mRNA).
Here, i represents a gene in the circuit, j represents its predecessor. α and α0 are the dimensionless maximum production rate and leakiness. n here equals to 2. β is the ratio of protein decay rate and mRNA decay rate. Bifurcation analysis is done by [2][3][4][15]. The results showed that a stable oscillation should satisfy the constrain that β>0.07 approximately, α>αbifurcation=r0n+1+r0 and r0=(2/(n-2))1/n. Otherwise, the result will be like Fig.3.
However, the equations above is still too ideal. In real situation, those parameters may be different and even fluctuate through time. If we solve the equations above with no change, the curve will be the same and this system won’t oscillate as is shown in Fig.3. Consider the situation that β is the most marked parameter, which can affect the oscillation frequency markedly. We assume that β satisfies the Gaussian distribution. The standard deviation of β is βΔ. Also, we have to admit that the standard deviation of β is beyond our ability to measure it with experiments, but after all it is still one of simulating the fluctuation. The interesting fact is that the system will always oscillate with even small deviation as is shown in Fig.4.
Fig. 3. (a) is the concentration of protein with time, (b) is the phase diagram of two protein. We can see that the trajectory will go along the line and the turn back to the steady point (red dot). The parameters are chosen as α=216, α₀=α/1000, β=1, n=2 following [7].
(b): The phase diagram of (a).
(c): The concentration of proteins with β=1.01, 0.99, and 1.0.
(d): The phase diagram of (c).
The other parameters are all the same as Fig.2. However, similar oscillation occurs if we add relative error in , α and α₀. Conclusion: the continuous oscillation depends on the relative error of parameters. Further reaserch can focus on bifurcation analysis of β. However, bigger relative error only increases the time to get to the limit cycle and it has little influence on the period of oscillation.
However, the equations above is still too ideal. In real situation, those parameters may be different and even fluctuate through time. If we solve the equations above with no change, the curve will be the same and this system won’t oscillate as is shown in Fig.3. Consider the situation that β is the most marked parameter, which can affect the oscillation frequency markedly. We assume that β satisfies the Gaussian distribution. The standard deviation of β is βΔ. Also, we have to admit that the standard deviation of β is beyond our ability to measure it with experiments, but after all it is still one of simulating the fluctuation. The interesting fact is that the system will always oscillate with even small deviation as is shown in Fig.4.
So far it seems good. The oscillation of the proteins that we want is here. However, this system that we have derived only works in a single cell. We have no reason to believe that clusters of cells’ proteins will have synchronized oscillation as is shown in Fig.5. Here, we introduce another parameter iₘₐₓ represents the cell number.
(b) shows that if we consider the fluctuation of different cells, the total concentration oscillates but the difference between the peak and valley concentration will be much smaller compared to one cell situation. It doesn’t seem good if the concentration of Melatonin won’t change strongly. Of course, we have to admit that the value of βΔ is hard to measure, but it is at least a good fluctuation. A similar case analyzed the influence of βΔ[11], and it showed that larger βΔ comes with bigger difficulty to synchronize. Here, we no longer talk about the influence of βΔ and consider it equals to 0.05 all the time.
Aiming to solve this problem, we introduced another function into the system: Quorum sensing. We can replace the equation in (1.5) with:
The third term is the quorum sensing term, with assumption that it follows a standard Michaelis-Menten kinetics. The concentration of Ai inside each cell is denoted by Sᵢ, which is also scaled by its Michaelis constant. κ is the maximum contribution to LacI transcription in the presence of saturating amounts of AI. On the other hand, the dynamics of intracellular Ai concentration is influenced by cell division’s dilution (degradation term), synthesis and the diffusion with intercellular medium. To model the membrane diffusion between cell and the medium we applied the picture of diffusion through a long, thin channel to membrane transport. Thus we expect that the flux through the membrane will be of the form
Here the permeation constant of solute, PS, is a number depending on both the membrane and the molecule whose permeation. In simple cases, the value of Pₛ roughly reflects the width of the pore, the thickness of the membrane (length of the pore), and the diffusion constant for the solute molecules. We can firstly imaging the cell as a perfect ball membrane with surface area A and volume V. The value of A and V is ~π μm2 and ~1 μm3. Data A, V and PS are taken from www.bioNumbers.org. Since
we can get that the concentration of Si’s diffusion obeys the equation (1.12) by solving the equations (1.8-1.11).
After adding the degradation and synthesis term and rewriting those redundant parameters, we get whole equation (1.13):
Here, we already defined a new parameter η called diffusion constant and let η=APₛ/V. k₀ and k₁ are the rate constant of degradation and synthesis (rescaled dimensionless constant). It contains three terms: degradation, synthesis and diffusion. As for the extracellular concentration of AI, with similar derivation, we can get:
Here ηₑₓₜ represents the diffusion constant if we consider the extracellular medium as the inside. Still for simplicity, we use the well-known quasi-steady-state approximation(QSSA) which is widely considered a good approximation to describe quorum sensing. Besides, we will use QSSA to replace quasi-steady-state approximation in what follows. Equation(1.15) is the main form of QSSA because we assume that dSₑ/dt=0. Equation(1.15) tells us that extracellular AI follows the evaluation of intracellular AI at all time.
Obviously, Q is linearly proportional to the cell density and its value lies between 0 and 1. With equation (1.15), we can reduce one dimension since it is hard to quantitatively describe the concentration of extracellular AI.
This equation system has(7×imax+1) dimensions. Hence, with the increase of imax, equation (1.16) requires more and more time to solve it numerically. Here, we will set imax=20, and this is high enough for us to eliminate the accidental error caused by Gaussian Distribution parameter β as much as possible. Here, the number of equations to be numerically solved is 141. So let’s take a look at what we got solving (1.16) by changing value Q (cell density) as is shown in Fig. 6, 7 and 8. Here, we showed the evaluation of extracellular AI, which is a good way to analysis the stability of quorum sensing. If the extracellular AI oscillates in a stable period, it means that quorum sensing can synchronize the oscillation.
The reason is that we want to determine the time it takes for Se to reach a relative steady sate. By solving equation (1.17) with the rest of the equations in (1.14) and (1.16), we can obtain the evaluation of Se. For simplicity, we assume that there is only one cell in the medium, which means imax=1 in equation (1.14) and (1.16). Hence, our problem becomes much more simple: we only need to calculate the ratio of Se and Si and estimate the time to reach steady value. Stable value means that Q won’t oscillate sharply like the concentration of those proteins. The result of our calculation is shown in Fig.9. Here, we assume the degradation constant of extracellular AI k₂ is equal to the degradation constant of intracellular AI k₁. Besides, Obviously, β here will have no Gaussian Distribution if there is only one cell in the medium.
(a)
(b)
(c)
Fig.6. The parameters are chosen as Q=0.01, κ=20,
k0=1, k1=0.01 and others are the same as Fig.5. (a) is the concentration of
protein CI in different cells.
(b) is the concentration of protein CI
and
the average of every cell’s protein CI.
(c) is the concentration of
extracellular AI. Here, κ, k1, k2 are also hard to measure in our lab, so we
just followed [16].
a
b
c
Fig.7. The parameters are chosen as Q=0.4, and others are the same as Fig.6. (a) is the concentration of protein CI in different cells. (b) is the concentration of protein CI and the average of every cell’s protein CI. (c) is the concentration of extracellular AI.
a
b
c
Fig.8. The parameters are chosen as Q=0.8, and others are the same as Fig.5. (a) is the concentration of protein CI in different cells. (b) is the concentration of protein CI and the average of every cell’s protein CI. (c) is the concentration of extracellular AI. Conclusion: With Q become larger, which also means larger influence of quorum sensing or cell density, the system tends to synchronize. The concentration of Average protein CI will be more like a single cell situation. It is good to see this. We now can expect our Melatonin to express stably and strongly during the time we want.
So far, we have proved that repressilator system plus quorum sensing can synchronize the oscillation of a cluster of cells. However, there are still many aspects that we didn’t consider, since the real situation is much more complex than our simple model. In order to improve the system further, we intend to analyze the influence of QSSA. Before that, we may ask some questions about QSSA. Question 1: how long does the system take to reach quasi-steady-state or how long do intracellular travel through the cell membrane and the extracellular AI becomes synchronized with intracellular AI ? Question 2: If we consider the time that it takes to reach quasi-steady-state, what will happen to the system’s behavior? Through our research, it turned out that QSSA made the system lose some behavior.
To answer the question 1, we can firstly include equation (1.14) into the equation system instead of using QSSA (it ignores the differential equation of Se). Whereas, we need to rewrite equation (1.14) as
With the result of Fig.9 we successfully estimated the time for intracellular AI. Hence, we set the delay time as τ=4.
With the result of the delay time τ, we can introduce delay differential equation to describe the behavior of the system. What is the definition of delay differential equation? In mathematics, delay differential equations (DDEs) are a type of differential equation in which the derivative of the unknown function at a certain time is given in terms of the values of the function at previous times. Therefore, we rewrite the equation of Si (1.13) as:
The term Sₑ₍t-τ₎ means that the concentration of intracellular AI at time t depends on the concentration of extracellular AI at time t-τ. This change of equation is used to describe the time delay for intracellular AI to travel through membrane and reach steady state with extracellular AI. Then we can get the following results with the new version of equations (1.16) by changing the value Q (cell density):
Interesting fact: owing to the delay time to reach QSS, synchronization by quorum sensing becomes less effective. The phase lag of different cells will not decrease like the original equations in chapter 1.4, and fluctuation of concentration is everywhere. The phase lag brought by delay time will hamper the synchronization because the cell only feels the extracellular AI a moment ago. Although the result is less satisfying, but our new equations (1.18) is at least closer to the real situation. On the other hand, if we make the period of oscillation long enough, the fluctuation of Melatonin will be less. According to our result here, our project must make sure the cells that produce Melatonin must gather together to let quorum sensing synchronize their oscillation period.
With the analysis of chapter 1.6, we have already got a basic image of the behavior of the repressilator. Aiming to make our project more reliable, we need to control the period of oscillation. In our project, we intend to make the production of Melatonin follow people’s biological clock. Nevertheless, according to the results in chapter 1.6, the period with β=1.0 is around 12 times mRNA lifetime, which yields around 1 hour if we set mRNA lifetime equals to 5 minutes. Unfortunately, this is still hard to reach our design. Therefore, we are going to analyze the controlling parameters of period. Apparently, β is the marked parameter. The other parameters like α₀, n, κ andη mainly affect the expressing strength (concentration of peak value), while β can change the period of proteins. So, we set β=2.0, 1.0, 0.5, 0.2, 0.1 respectively and the results are shown in Fig.13. Of course, β here means the mean value, and the standard deviation βΔ still equals to 0.05.
From the Fig.13, we can apparently
conclude that the period will become
longer with the decrease of β. However, longer period comes along with
unsteadiness. We can see that if we set β<0.2, the system won’t even
oscillates (some of the cell). We can set βₘᵢₙ=0.2 as the critical value.
Below βₘᵢₙ, where mRNA decay rate is 5 times as much as the protein decay
rate, we’d better avoid that if we want our Melatonin produce steadily.
Approximately, we can make our mRNA decay a little bit faster like 2 to 4
times will be good. The period will increase roughly from one hour to 1.5
hours and 3 hours. Objectively speaking, this is still not up to standard.
But at least we can figure out other ways to increase mRNA lifetime. If we
can lengthen the mRNA lifetime to 4 times as much as the original one, we
may hopefully reach our aim.
What’s more, we can analyze the phase
diagram of protein CI in one cell and
average protein CI in every cell. The results are in Fig.14.
In order to see the oscillation of Melatonin intuitively, our team linked CFP gene to the CI gene. We set imax=900, which suggests that we have a 6301 equations system to be solved. We improved explicit Runge-Kutta method by adding the time delay term into the algorithm so that we can solve a DDE system. Fig.15 is a experimental picture from our team. Those green dots represent E.coli, and they are diluted so that we can see it clearly.
The simulation of repressilator is shown in Fig.16. There are three groups of figures. The left images are arrayplots. Each pixel represents a cell and the intensity of the fluorescence or concentration of Melatonin is represented as green color. The Right images are the average intensity or concentration of Melatonin.
So far, our modeling shows that with high Q value (means high cell density for quorum sensing) the concentration of the target protein or Melatonin will oscillate even there is fluctuation and time delay to the system. To be honest, it’s hard to judge the reliability of the modeling of repressilator, and some of the parameters we used may not be that accurate due to the fluctuations of the cells’ physical property. Biology system is complex, and we still have much room to improve our model like considering the concentration impact of cell division[1][8] or introducing stochastic differential equations[5]. However, we do have the confidence that our modeling can be an effective and reasonable reference to design our project or similar projects.
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Phys Biol. 2015;12(6):066003.
2. BUSE O, KUZNETSOV A, ́REZ RAP. Existence of limit cycles in the repressilator
equations. Journal of Bifurcation and chaos. 2009;19.
3. Buse O, Perez R, Kuznetsov A. Dynamical properties of the repressilator
model. Phys Rev E Stat Nonlin Soft Matter Phys. 2010;81(6 Pt 2):066206.
4. BUZZI. CA, LLIBRE. J. HOPF BIFURCATION IN THE FULL REPRESSILATOR EQUATIONS.
2010.
5. Cai X. Exact stochastic simulation of coupled chemical reactions with delays.
J Chem Phys. 2007;126(12):124108.
6. Churilov AN, Medvedev A, Zhusubaliyev ZT. Impulsive Goodwin oscillator with
large delay: Periodic oscillations, bistability, and attractors. Nonlinear
Analysis: Hybrid Systems. 2016;21:171-83.
7. Elowitz MB, Leibler S. A synthetic oscillatory network of transcriptiona.
Nature. 2000;403.
8. Gonze D. Modeling the effect of cell division on genetic oscillators. J Theor
Biol. 2013;325:22-33.
9. Goodwin BC. Oscillatory Behavior in Enzymatic Control Process. Advances in
Enzyme Regulation. 1965.
10. J.D.Dockery, J.P.Keener. A mathematical model for quorum sensing in
pseudomonas aeruginosa. Mathematical Biology. 2001.
11. Jordi Garcia-Ojalvo MBE, and Steven H. Strogatz. Modeling a synthetic
multicellular clock: Repressilators coupled by quorum sensing. PNAS.
2004;101.
12. Kopell DMaN. Synchronizing Genetic Relaxation Oscillators by Intercell
Signaling. PNAS. 2002;99.
13. Ling G, Guan ZH, He DX, Liao RQ, Zhang XH. Stability and bifurcation
analysis of new coupled repressilators in genetic regulatory networks with
delays. Neural Netw. 2014;60:222-31.
14. Muller S, Hofbauer J, Endler L, Flamm C, Widder S, Schuster P. A generalized
model of the repressilator. J Math Biol. 2006;53(6):905-37.
15. O'Brien EL, Itallie EV, Bennett MR. Modeling synthetic gene oscillators.
Math Biosci. 2012;236(1):1-15.
16. Potvin-Trottier. L, Lord1. ND, Vinnicombe. G, Paulsson. J. Synchronous
long-term oscillations in a synthetic gene circuit. Nature. 2016;538.
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synthetic genetic oscillators. J R Soc Interface. 2010;7(52):1503-24.
18. Shampine LF, Thompson S. Numerical Solution of Delay Differential Equations.
2009:1-27.
19. Philip Nelson. Biological Physics: Energy, Information, Life.


In this notebook we shall create a continuous Hidden Markov Model [1] for an electrical appliance. Problem description:
In all it matches the description of a continuous Hidden Markov Model. The different components of the Discrete HMM are as follows:
Next, we import the basic set of libraries used for matrix manipulation and for plotting.
import numpy as np
import matplotlib.pyplot as plt
import matplotlib
#Setting Font Size as 20
matplotlib.rcParams.update({'font.size': 20})
Next, we define the different components of HMM which were described above.
pi=np.array([.9,.1])
A=np.array([[.99,.01],[.1,.9]])
B=np.array([{'mean':0,'variance':1},{'mean':170,'variance':4}])
Now based on these probability we need to produce a sequence of observed and hidden states. We use the notion of weighted sampling, which basically means that terms/states with higher probabilies assigned to them are more likely to be selected/sampled. For example,let us consider the starting state. For this we need to use the pi matrix, since that encodes the likiliness of starting in a particular state. We observe that for starting in Fair state the probability is .667 and twice that of starting in Biased state. Thus, it is much more likely that we start in Fair state. We use Fitness Proportionate Selection [3] to sample states based on weights (probability). For selection of starting state we would proceed as follows:
'''
Returns next state according to weigted probability array. Code based on Weighted random generation in Python [4]
'''
def next_state(weights):
choice = random.random() * sum(weights)
for i, w in enumerate(weights):
choice -= w
if choice < 0:
return i
We test the above function by making a call to it 1000 times and then we try to see how many times do we get a 0 (Fair) wrt 1 (Biased), given the pi vector.
count=0
for i in range(1000):
count+=next_state(pi)
print "Expected number of Fair states:",1000-count
print "Expected number of Biased states:",count
Thus, we can see that we get approximately twice the number of Fair states as Biased states which is as expected.
Next, we write the following functions:
def create_hidden_sequence(pi,A,length):
out=[None]*length
out[0]=next_state(pi)
for i in range(1,length):
out[i]=next_state(A[out[i-1]])
return out
def create_observation_sequence_continuous(hidden_sequence,B):
length=len(hidden_sequence)
out=[None]*length
for i in range(length):
out[i]=np.random.normal(B[hidden_sequence[i]]['mean'],B[hidden_sequence[i]]['variance'],1)
return out
Thus, using these functions and the HMM paramters we decided earlier, we create length 1000 sequence for hidden and observed states.
hidden=np.array(create_hidden_sequence(pi,A,1000))
observed=np.array(create_observation_sequence_continuous(hidden,B))
plt.figsize(16,10);
plt.subplot(2,1,1)
plt.title('Observed Power draw')
plt.ylabel('Power (W)');
plt.xlabel('Sample #');
plt.plot(observed)
plt.subplot(2,1,2);
plt.fill_between(range(len(hidden)),hidden,0,alpha=0.5)
plt.plot(hidden,linewidth=3);
plt.ylabel('State');
plt.xlabel('Sample #');
plt.title('0- Compressor Off, 1- Compressor On');
plt.tight_layout()


| Author | Jos de Jong, Almende B.V. |
| Webpage | Chap Links Library |
| License | Apache License, Version 2.0 |
Graph3d is an interactive visualization chart to draw data in a three dimensional graph. You can freely move and zoom in the graph by dragging and scrolling in the window. Graph3d also supports animation of a graph.
The graph works smooth on any modern browser for data up to 10.000 points.
The Graph is developed as a Google Visualization Chart in javascript. It runs on all modern browsers without additional requirements. Graph is tested on Firefox 3.6+, Safari 5.0+, Chrome 6.0+, Opera 10.6+, Internet Explorer 9+.
To get started with Graph3d, download graph3d.zip, and unzip the contents in a subfolder graph3d on your site. Examples can be found in the examples directory. The possiblities of Graph3d can be tested on the playground.
Here a graph example. Click and drag to move the graph, scroll to zoom the graph.
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">   <title>Graph 3D demo</title>

Graph3d is no built-in visualization of Google.
To load Graph3d, download the file
graph3d.zip
,
and unzip it in your html page such that the files are located in a subfolder graph3d.
Include the google API and the following files in the head of your html code:

The google visualization needs to be loaded in order to use DataTable.
google.load("visualization", "1"); google.setOnLoadCallback(drawVisualization); function drawVisualization() { // load data and create the graph here }The class name of the Graph3d is
links.Graph3d
var graph = new links.Graph3d(container);After being loaded, the graph can be drawn via the function
draw()
,
provided with data and options.
graph.draw(data, options);where data is a
DataTable
, and options is a name-value map in the JSON format.
Graph3d requires a data table with tree to five columns, depending on the chosen style and animation. The first three columns must contain the location coordinates for x-axis, y-axis, and z-axis. The forth column is optional, and can contain a data value. The last column (this can be the fourth or fifth column) and can contain filter values used for animation.
Note that the column labels can be changed (for example instead of 'value'
one can use 'Temperature'
).
The data columns are defined as:
| Name | Type | Required | Description |
|---|---|---|---|
| x | number | yes | Location on the x-axis. |
| y | number | yes | Location on the y-axis. |
| z | number | yes | Location on the z-axis. |
| value | number | no | The data value, required for graph styles dot-color and
dot-size .
|
| filtervalue | anytype | no | Filter values used for the animation. This column may have any type, such as a number, string, or Date. |
Graph3d supports the following styles to display data in three dimensions:
dot
, dot-line
, line
, grid
,
and surface
.
The data table for these styles is constructed as follows.
var data = new google.visualization.DataTable(); data.addColumn('number', 'x'); data.addColumn('number', 'y'); data.addColumn('number', 'z'); // the data value, visualized as a height at the z-axis // and by a color. data.addRow([2.3, 5.2, 102.1]); // ...
Graph3d supports the following styles to display data in four dimensions:
dot-color
, dot-size
.
The data table for these styles is constructed as follows.
var data = new google.visualization.DataTable(); data.addColumn('number', 'x'); data.addColumn('number', 'y'); data.addColumn('number', 'z'); data.addColumn('number', 'value'); // the data value, visualized by a color or size data.addRow([2.3, 5.2, 102.1, 45.2]); // ...
If an extra column with filter values is provided in the data table, Graph3d will use these values for animation. The filter values are grouped and each group represents one animation frame. When animating, Graph3d loops through the distinct filter values, and draws all data points which have the current filter value.
For example, to create an animation with three frames, first add all datapoints for the first frame with a filtervalue 1. Next, add the datapoints for the second frame and give them a filtervalue 2. Last, add the datapoints for the third frame and give them a filtervalue of 3. Now, when the Graph3d is loaded, a slider with buttons play/next/previous will be drawn below the graph, where one can loop through the three frames.
To create an animation, add an extra column to the data table. This column may have any type (number, date, string, ...).
var data = new google.visualization.DataTable(); data.addColumn('number', 'x'); data.addColumn('number', 'y'); data.addColumn('number', 'value'); data.addColumn('number', 'filtervalue'); // Optional column with filter values for animation data.addRow([2.3, 5.2, 102.1, 23]); // ...
Options can be used to customize the graph. Options are defined as a JSON object. All options are optional.
options = {width: "100%", height: "400px", style: "surface" };
The following options are available.
| Name | Type | Default | Description |
|---|---|---|---|
| animationInterval | number | 1000 | The animation interval in milliseconds. This determines how fast the animation runs. |
| animationPreload | boolean | false | If false, the animation frames are loaded as soon as they are requested.
if animationPreload is true, the graph will automatically load
all frames in the background, resulting in a smoother animation as soon as
all frames are loaded. The load progress is shown on screen. |
| animationAutoStart | boolean | false | If true, the animation starts playing automatically after the graph is created. |
| backgroundColor | string or Object | "white" | The background color for the main area of the chart. Can be either a simple HTML color string, for example: 'red' or '#00cc00', or an object with the following properties. |
| backgroundColor.stroke | string | "gray" | The color of the chart border, as an HTML color string. |
| backgroundColor.strokeWidth | number | 1 | The border width, in pixels. |
| backgroundColor.fill | string | "white" | The chart fill color, as an HTML color string. |
| cameraPosition | Object | {"horizontal": 1.0, "vertical": 0.5, "distance": 1.7} | Set the initial rotation and position of the camera.
The object cameraPosition contains three parameters:
horizontal , vertical , and distance .
Parameter horizontal is a value in radians and can have any
value (but normally in the range of 0 and 2*Pi).
Parameter vertical is a value in radians between 0 and 0.5*Pi.
Parameter distance is the (normalized) distance from the
camera to the center of the graph, in the range of 0.71 to 5.0. A
larger distance puts the graph further away, making it smaller.
All parameters are optional.
|
| height | string | "400px" | The height of the graph in pixels or as a percentage. |
| keepAspectRatio | boolean | true | If keepAspectRatio is true, the x-axis and the y-axis
keep their aspect ratio. If false, the axes are scaled such that they
both have the same, maximum with. |
| showAnimationControls | boolean | true | If true, animation controls are created at the bottom of the Graph. The animation controls consists of buttons previous, start/stop, next, and a slider showing the current frame. Only applicable when the provided data contains an animation. |
| showGrid | boolean | true | If true, grid lines are draw in the x-y surface (the bottom of the 3d graph). |
| showPerspective | boolean | true | If true, the graph is drawn in perspective: points and lines which are further away are drawn smaller. Note that the graph currently does not support a gray colored bottom side when drawn in perspective. |
| showShadow | boolean | false | Show shadow on the graph. |
| style | string | "dot" | The style of the 3d graph. Available styles:
dot ,
dot-line ,
dot-color ,
dot-size ,
line ,
grid ,
or surface |
| valueMax | number | none | The maximum value for the value-axis. Only available in combination
with the styles dot-color and dot-size . |
| valueMin | number | none | The minimum value for the value-axis. Only available in combination
with the styles dot-color and dot-size . |
| verticalRatio | number | 0.5 | A value between 0.1 and 1.0. This scales the vertical size of the graph When keepAspectRatio is set to false, and verticalRatio is set to 1.0, the graph will be a cube. |
| width | string | "400px" | The width of the graph in pixels or as a percentage. |
| xCenter | string | "55%" | The horizontal center position of the graph, as a percentage or in pixels. |
| xMax | number | none | The maximum value for the x-axis. |
| xMin | number | none | The minimum value for the x-axis. |
| xStep | number | none | Step size for the grid on the x-axis. |
| yCenter | string | "45%" | The vertical center position of the graph, as a percentage or in pixels. |
| yMax | number | none | The maximum value for the y-axis. |
| yMin | number | none | The minimum value for the y-axis. |
| yStep | number | none | Step size for the grid on the y-axis. |
| zMin | number | none | The minimum value for the z-axis. |
| zMax | number | none | The maximum value for the z-axis. |
| zStep | number | none | Step size for the grid on the z-axis. |
Graph3d supports the following methods.
| Method | Return Type | Description |
|---|---|---|
| animationStart() | none | Start playing the animation. Only applicable when animation data is available. |
| animationStop() | none | Stop playing the animation. Only applicable when animation data is available. |
| draw(data, options) | none | Loads data, sets the provided options, and draws the 3d graph. |
| getCameraPosition() | An object with parameters horizontal ,
vertical and distance |
Returns an object with parameters horizontal ,
vertical and distance ,
which each one of them is a number, representing the rotation and position
of the camera. |
| redraw() | none | Redraw the graph. Useful after the camera position is changed externally, when data is changed, or when the layout of the webpage changed. |
| setSize(width, height) | none | Parameters width and height are strings,
containing a new size for the graph. Size can be provided in pixels
or in percentages. |
| setCameraPosition (pos) | {"horizontal": 1.0, "vertical": 0.5, "distance": 1.7} | Set the rotation and position of the camera. Parameter pos
is an object which contains three parameters: horizontal ,
vertical , and distance .
Parameter horizontal is a value in radians and can have any
value (but normally in the range of 0 and 2*Pi).
Parameter vertical is a value in radians between 0 and 0.5*Pi.
Parameter distance is the (normalized) distance from the
camera to the center of the graph, in the range of 0.71 to 5.0. A
larger distance puts the graph further away, making it smaller.
All parameters are optional.
|
Graph3d fires events after the camera position has been changed.
The event can be catched by creating a listener.
Here an example on how to catch a camerapositionchange
event.
function oncamerapositionchange(event) { alert("The camera position changed to:\n" + "Horizontal: " + event.horizontal + "\n" + "Vertical: " + event.vertical + "\n" + "Distance: " + event.distance); } google.visualization.events.addListener(mygraph, 'camerapositionchange', oncamerapositionchange);
The following events are available.
| name | Description | Properties |
|---|---|---|
| camerapositionchange | The camera position changed. Fired after the user modified the camera position
by moving (dragging) the graph, or by zooming (scrolling),
but not after a call to setCameraPosition method.
The new camera position can be retrieved by calling the method
getCameraPosition . |
|
| ready | The graph is ready for external method calls. If you want to interact with the graph, and call methods after you draw it, you should set up a listener for this event before you call the draw method, and call them only after the event was fired. | none |
All code and data are processed and rendered in the browser. No data is sent to any server.


CIS-157 Home: http://www.c-jump.com/bcc/c157c/c157syllabus.html
There are three types of errors that may occur in Java programming:
Syntax errors (or compile-time errors) -- violate Java syntax rules or rules for Java statements (e.g. code may require an exception handler.)
Runtime errors -- the syntax is okay, but these errors throw exceptions that stop the execution of the application.
Logic errors -- the code that produces the wrong results without syntax or runtime errors, e.g. wrong formula to convert inches to centimeters.
Misspelling keywords.
Forgetting to declare a data type for a variable.
Forgetting an opening or closing parenthesis, bracket, brace, or comment character.
Forgetting to code a semicolon at the end of a statement.
Forgetting an opening or closing quotation mark.
Using a reserved word, global property, or global method as an identifier.
Not checking the value before processing it. For example, user enters non-numeric value instead of a number.
Division by zero
Misspelling or incorrectly capitalizing an identifier, then using a wrong variable as a result.
Using one equals sign (=) instead of two (==) when testing numeric and boolean values for equality.
Using two equals signs (==) instead of equals()/equalsIgnoreCase() methods to test two strings for equality.
The Java programming language uses exceptions to handle errors and other exceptional events
Some of the classes in the Exception hierarchy
Exception RuntimeException NoSuchElementException InputMismatchException IllegalArgumentException NumberFormatException ArithmeticException NullPointerException
After an InputMismatchException has been thrown, the console output window might look like this:
Exception in thread "main" java.util.InputMismatchException at java.util.Scanner.throwFor(Scanner.java:909) at java.util.Scanner.next(Scanner.java:1530) at java.util.Scanner.nextDouble(Scanner.java:2456) at InvoiceApp.main(InvoiceApp.java:20)
The program prints a stack trace and exits.
Four methods that might throw an exception:
Class Method Throws --------- ------------------- ----------------------- Scanner nextInt() InputMismatchException Scanner nextDouble() InputMismatchException Integer parseInt(String) NumberFormatException Double parseDouble(String) NumberFormatException
The syntax for the try statement
try { statements } catch (ExceptionClass exceptionName) { statements }
A try statement anticipates that an exception may occur
A catch block to provide a handler for the exception
Two ways to import the InputMismatchException class
import java.util.InputMismatchException; import java.util.*;
A try statement that catches an InputMismatchException
double subtotal = 0.0; try { System.out.print("Enter subtotal: "); subtotal = sc.nextDouble(); } catch (InputMismatchException e) { sc.next(); // discard the incorrectly entered double System.out.println( "Error! Invalid number. Try again.\n"); continue; // jump to the top of the loop }
Multiple catch blocks are allowed:
try { } catch (ExceptionType name) { } catch (ExceptionType name) { }
For example,
try { } catch (FileNotFoundException e) { System.err.println("FileNotFoundException: " + e.getMessage()); throw new SampleException(e); } catch (IOException e) { System.err.println("Caught IOException: " + e.getMessage()); }
The finally block executes
when the try block exits normally, or
when an exception occurs.
Therefore, the finally block always executes when the try block exits.
try { } catch (ExceptionType name) { } catch (ExceptionType name) { } finally { // always executes }
The finally block is a key tool for preventing resource leaks. Place the code in a finally block when closing a file or recovering other resources
There are methods of the Scanner class that you can use to validate data:
hasNext( )
hasNextInt( )
hasNextDouble( )
nextLine( )
double subtotal = 0.0; System.out.print("Enter subtotal: "); if (sc.hasNextDouble()) { subtotal = sc.nextDouble(); } else { sc.nextLine(); // discard the entire line System.out.println( "Error! Invalid number. Try again.\n"); continue; // jump to the top of the loop }
Console output:
Enter subtotal: $100 Error! Invalid number. Try again. Enter subtotal:
if (customerType != null)
{
if (customerType.equals("R"))
discountPercent = .4;
}
Code that gets a valid double value within a specified range
Scanner sc = new Scanner(System.in); double subtotal = 0.0; boolean isValid = false; while (isValid == false) { // get a valid double value System.out.print("Enter subtotal: "); if (sc.hasNextDouble()) { subtotal = sc.nextDouble(); isValid = true; } else { System.out.println( "Error! Invalid number. Try again."); } sc.nextLine(); // discard any other data entered on the line // check the range of the double value if (isValid == true && subtotal <= 0) { System.out.println( "Error! Number must be greater than 0."); isValid = false; } else if (isValid == true && subtotal >= 10000) { System.out.println( "Error! Number must be less than 10000."); isValid = false; } }
A method that gets a valid numeric format
public static double getDouble(Scanner sc, String prompt) { double dbl = 0.0; boolean isValid = false; while (isValid == false) { System.out.print(prompt); if (sc.hasNextDouble()) { dbl = sc.nextDouble(); isValid = true; } else { System.out.println( "Error! Invalid number. Try again."); } sc.nextLine(); // discard any other data } return dbl; }
Each Java program must follow this rule:
if a block of code can throw an exception, such block of code must be
(a) wrapped by a try statement that catches exceptions and handles them in the corresponding catch blocks.
try { //a block of code that can throw an exception } catch (ExceptionType name) { }
(b) enclosed in a method with the throws clause, for example,
public void saveFile() throws IOException {
//a block of code that can throw an exception
}///saveFile
Otherwise, if Catch or Specify requirement is not honored, the code will not compile.


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#include <setup_payload/SetupPayload.h>
Public Member Functions | |
| OptionalQRCodeInfoExtension () | |
| Public Member Functions inherited from chip::OptionalQRCodeInfo | |
| OptionalQRCodeInfo () | |
Public Attributes | |
| int64_t | int64 |
| uint64_t | uint32 |
| uint64_t | uint64 |
| Public Attributes inherited from chip::OptionalQRCodeInfo | |
| uint8_t | tag |
| the tag number of the optional info More... | |
| enum optionalQRCodeInfoType | type |
| the type (String or Int) of the optional info More... | |
| std::string | data |
| the string value if type is optionalQRCodeInfoTypeString, otherwise should not be set More... | |
| int32_t | int32 |
| the integer value if type is optionalQRCodeInfoTypeInt, otherwise should not be set More... | |
|
inline |
| int64_t chip::OptionalQRCodeInfoExtension::int64 |
| uint64_t chip::OptionalQRCodeInfoExtension::uint32 |
| uint64_t chip::OptionalQRCodeInfoExtension::uint64 |


Chapter 5 Intro to NEON Culmination Activity
- What is the temporal frequency of observations in the data you decided was of interest? How do the data align to answer a central question? What challenges did you run into when investigating these data? How will you address these challenges and document your code? One to two paragraphs
5.1 Intro to NEON Culmination Activity
Due before we start Chapter 3: USA-NPN >>>>>>> upstream/master
Write up a 1-page summary of a project that you might want to explore using NEON data over the duration of this course. Include:
- the types of NEON (and other data) that you will need to implement this project, including data product id numbers.
- If in your NEON coding lab part 2 you highlighted challenges to using these data, discuss methods to address those challenges. *e.g. If your site doesn’t yet have a long data recocrd, is it located close to a longer lived site from another network? (LTER, Ameriflux, LTAR etc)
- One high-level summary graphic including all of your data from the NEON Coding Lab Part 2
Save this summary as you will be refining and adding to your ideas over the course of the semester.


Which conversation would you like to convert? {% for name in list_of_names[:-1] %} {% if name[0] != '.' %} {{ name.split("_", 1)[0] }} {%endif%} {%endfor%}


Trajectory package¶
mesohops.dynamics.hops_trajectory class¶
-
class
HopsTrajectory
(system_param, eom_param={}, noise_param={}, hierarchy_param={}, integration_param={'INCHWORM': False, 'INCHWORM_MIN': 5, 'INTEGRATOR': 'RUNGE_KUTTA'})¶ Bases:
object
HopsTrajectory is the class that a user should interface with to run a single trajectory calculation.
-
inchworm_integrate
(self, state_update, aux_update, tau)¶ This function performs inchworm integration.
- Parameters
- 1. state_update
- list_state_newlist
list of new states
- state_stablelist
list of stable states in the current basis
- list_add_statelist
list of new states that were not in previous state list
- 2. aux_update
- aux_newlist
list of new auxiliaries
- stable_auxlist
list of stable auxiliaries in the current basis
- add_auxlist
list of new auxiliaries that were not in the previous aux list
- 3. taufloat
the time step
- Returns
- state_update
- list_state_newlist
list of new states
- state_stablelist
list of stable states in the current basis
- list_add_statelist
list of new states that were not in previous state list
- aux_update
- aux_newlist
list of new auxiliaries
- stable_auxlist
list of stable auxiliaries in the current basis
- add_auxlist
list of new auxiliaries that were not in the previous aux list
- 3. phinp.array
the full state of the hierarchy normalized if appropriate
-
initialize
(self, psi_0, store_aux=False)¶ This function initializes the trajectory module by ensuring that each sub-component is prepared to begin propagating a trajectory.
- Parameters
- 1. psi_0np.array
Wave function at initial time
- Returns
- None
-
make_adaptive
(self, delta_h=0.0001, delta_s=0.0001)¶ This is a convenience function for transforming a not-yet-initialized HOPS trajectory from a standard hops to an adaptive HOPS approach.
- Parameters
- 1. delta_hfloat < 1
The value of the adaptive grid for the hierarchy of auxiliary nodes
- 2. delta_sfloat < 1
The value of the adaptive grid in the system basis
- Returns
- None
-
normalize
(self, phi)¶ This is the function that re-normalizes the wave function at each step to correct for loss of norm due to finite numerical accuracy
- Parameters
- 1. phinp.array
the current full state of the hierarchy
- Returns
- 1. phinp.array
the full state of the hierarchy normalized if appropriate
-
propagate
(self, t_advance, tau)¶ This is the function that perform integration along fixed time-points. The kind of integration that is performed is controlled by ‘step’ which was setup in the initialization.
- Parameters
- 1. t_advancefloat
How far out in time the calculation will run
- 2. taufloat
the time step
- Returns
- None
-
mesohops.dynamics.hops_storage class¶
-
class
AdaptiveTrajectoryStorage
¶ Bases:
mesohops.dynamics.hops_storage.TrajectoryStorage
This is an object that manages storing information for a HOPS trajectory.
-
class
TrajectoryStorage
¶ Bases:
object
This is an object that manages storing information for a HOPS trajectory.


TABLE OF CONTENT
A. GS1 Related B. GS2 Related Polity 1. Dr. Mahesh Sharma launches implementation of ‘National Mission on Cultural Mapping of India’ from Goverdhan Block, Mathura 2. No-fly list norms likely in July next week, says Government 3. No Aadhaar, no banking and threat to privacy: Do you have a choice? B. GS2 Related International Relations 1. Indo-Afghan air cargo plane to fly over Pak 2. ICJ rejected India’s request to delay Jadhav’s case, says Pakistan 3. India, China hold talks for strengthening strategic partnership C. GS3 Related Economics 1. Indians have 'rather few' deposits: Swiss banks 2. Secrecy must for automatic info exchange, Swiss banks tell India D. GS4 Related E. Concepts-in-News: Related Concepts to Revise/Learn F. Bills/Acts/Schemes/Orgs in News G. Practice Questions for UPSC Prelims Exam
UPSC Current Affairs 2017: News Analysis
A. GS1 Related
Nothing here for Today!!!
B. GS2 Related
Features of the scheme:
- Scheme is set to cover all blocks of the country, involving a total of 6.40 lakh villages over the span of next 3 years
- This Mission is part of the ‘Ek Bharat Shreshtha Bharat’
- Ministry of Culture launched it in the year of commemoration of the birth centenary of Pandit Deen Dayal Upadhyay, who hailed from Mathura.
- The Cultural Mapping of India portal will serve as a repository/consolidated database of information about cultural assets and resources i.e. a cultural inventory at one place for essential planning, sustainable economic development and for preserving the scattered and near extinct art forms.
Key Point:
- The mission aims at converting the vast and widespread cultural canvas of India into an objective cultural map, designing a mechanism to fulfil the aspirations of the whole artist community of the nation and preserving the rich cultural heritage of this country in the form of a cultural repository of artists and art forms.
- Mission encompasses data mapping, demography building formalising the processes and bringing all the cultural activities under one web based umbrella for better results.
- The Mission also seeks to open a direct channel of communication of artists with the Government and peer to peer communication among artists for talent honing and handholding of each other.
Main vision: no cultural talent or heritage should remain unattended and if it is talent, it should be nurtured and if it is a heritage, it should be conserved and used as an icon to learn from the past, and also to propagate our cultural talent across all boundaries.
2. No-fly list norms likely in July next week, says Government
In news:
- The norms for no-fly list to rein in unruly passengers are expected to be ready early next month, the government said.
- The civil aviation ministry has already come out with draft rules for a ‘national no-fly list’ of unruly passengers for all domestic carriers, under which the flying ban could extend from at least three months to an indefinite period.
- As per the draft norms, the national no-fly list will include names of passengers identified as unruly after an inquiry by a committee constituted by a particular airline.
- A person identified as a threat by security agencies would also be included in this list.
- While the list is characterised as ‘national’ and would have data on disruptive passengers from all airlines, the ban recommended by the committee is not mandatory for all airlines to follow.
- The government had recommended three levels of unruly behaviours, each with a corresponding duration of flying ban.
- The first level of misdemeanour includes disruptive behaviour such as physical gestures, verbal harassment and unruly behaviour because of inebriation. This level of offence would carry a flying ban of three months.
- The second level relates to physically abusive behaviour such as pushing, hitting, grabbing, inappropriate touching or sexual harassment. Such actions could attract a six—month ban.
- The third category pertains to life threatening behaviour such as damage to aircraft operating system, physical violence and attempted breach of flight crew compartment. In such instances, the ban could be for two years or an indefinite period.
- If a passenger repeats the same degree of offence, he or she would be banned for twice the period of the previous ban.
3. No Aadhaar, no banking and threat to privacy: Do you have a choice?
Context:
- The government has made Aadhaar mandatory for access to banking and filing I-T returns.
- But there are serious concerns about possible breach of privacy with private entities having access to Aadhaar data
Is Aadhaar mandatory?
- The Supreme Court has more than once told the government not to make Aadhaar mandatory for citizens.
- In 2015, on two occasions, the Supreme Court ruled that “it is not mandatory for a citizen to obtain an Aadhaar card” asking the government to advertise this prominently.
- The production of an Aadhaar card will not be condition for obtaining any benefits otherwise due to a citizen, the Supreme Court had said. However, the apex court has allowed the government to link various schemes including MNREGS, LPG, PDS, EPFO, Old Age Pension etc with Aadhaar.
- But, the Supreme Court ruling in 2015 clearly read, “… the Aadhaar card Scheme is purely voluntary and it cannot be made mandatory till the matter is finally decided by this Court one way or the other.”
- The apex court has set up a constitutional bench to hear Aadhaar case. The Aadhaar Act 2016 also does not make Aadhaar mandatory for citizens.
HOW GOVERNMENT MADE IT MANDATORY?
- Budget 2017 (passed by Parliament), which mandated seeding of Aadhaar number with Permanent Account Number (PAN).
- The amended Finance Act 2017. It made enrollment in Aadhaar compulsory for obtaining a PAN and filing Income Tax returns.
Implications:
- The Finance Act effectively meant that an earning member of Indian society is a potential criminal if s/he does not have an Aadhaar as the citizen would not be able to file I-T returns, which s/he is legally bound to do.
ARE AADHAAR DATA IN SAFE HANDS?
- Recently a report by the Centre for Internet Society said that more than 13 crore Aadhaar data were leaked, stolen or compromised.
- Section 29 of the Aadhaar Act prohibits sharing, publishing, displaying or posting publicly the core biometric information collected under the project except in “the interest of national security “. However, the Act does not state what constitutes national security.
- Section 57 of the Aadhaar Act, 2016 allows private companies to use the Aadhaar data to establish “identity of an individual for any purpose”.
Access to aadhaar data:
- There are several reports confirming that the Aadhaar data of Indian citizens are with companies like Accenture, Ernst and Young , L-1 Identity Solutions – the American biometric technology provider .
- The Unique Identification Authority of India (UIDAI) and the government allow access to Aadhaar data of people by these companies through Authentication User Agencies, which are both governmental and non-governmental entities.
RIGHT TO PRIVACY IN INDIA
- There is no specific law passed by Parliament for protection against breach of privacy of individuals in India.
- A bill, Privacy Bill, 2011 was drafted by the UPA-II government but it is hanging fire since then.
- Only th Information Technology Act, 2000 has some express provision guarding individuals against breach of privacy by corporate entities. Section 43A was inserted into the IT Act in 2008 which makes the companies compromising sensitive personal data liable to pay compensation.
- The right to privacy is dealt with under Article 21 of the Constitution which guarantees right to life and personal liberty.
COURTS ON RIGHT TO PRIVACY
- In 1954, an eight-judge bench in MP Sharma vs Satish Chandra case and in 1962 a six-judge bench of the Supreme Court in Kharak Singh vs State of Uttar Pradesh case had equated the right to privacy with right to personal liberty but rejected it as fundamental or constitutional right.
Category: INTERNATIONAL RELATIONS
1. Indo-Afghan air cargo plane to fly over Pak
In news:
- India and Afghanistan will operationalise a dedicated air cargo link over Pakistan in the next couple of days.
- Aim: help increase bilateral trade which was hampered by their troubled ties with Pakistan.
- Pakistan disallows Indian goods along the road route.
- The road link between the two countries passes through Pakistan, which allows only Afghanistan to send a limited amount of goods to India.
2. ICJ rejected India’s request to delay Jadhav’s case, says Pakistan
Context: Kulbhushan Jadhav’s case- Jadhav, was sentenced to death by a Pakistani military court in April.
In news:
- Pakistan claimed that the International Court of Justice (ICJ) rejected India’s request to delay proceedings of Kulbhushan Jadhav’s case until December.
- Pakistan through its consulate in Netherlands came to know that the ICJ had ordered India to submit a response by September 13.
What ICJ is supposed to do?
- The ICJ is supposed to conclude whether or not Jadhav can receive consular access, for which a time period of two to three months is more than enough to file a response.
Previously:
- In a hearing of the case on May 18, a 10-member bench at the The Hague-based ICJ restrained Pakistan from executing Jadhav.
- India moved the ICJ against the death penalty on May 8. The next day, the global court stayed the sentence as a provisional measure.
Pakistan stance: Its security forces arrested him from its restive Balochistan province on March 3 last year after he reportedly entered from Iran.
India’s stance : India maintains that he was kidnapped from Iran where he had business interests after retiring from the Navy.
3. India, China hold talks for strengthening strategic partnership
In news:
- Minister of state for external affairs VK Singh met foreign minister Wang Yi on the sidelines of the BRICS foreign ministers’ meeting.
- India said it looks forward to strengthen its strategic partnership and mutual dialogue with China as the two sides held talks here amid differences over a host of issues including the $50 billion CPEC and India’s NSG membership bid.
- BRICS foreign ministers’ meeting being held to finalise the agenda for this year’s BRICS (Brazil, Russia, India, China and South Africa) summit to be held in September in China’s Xiamen city.
- During the foreign ministers’ meet, China is expected to outline the agenda for this year’s BRICS summit which included efforts to seek common ground against terrorism.
C. GS3 Related
1. Indians have ‘rather few’ deposits: Swiss banks
Context: Illegal black money funds parked in Swiss bank.
In news:
- Indians have “ few deposits ” in Swiss banks compared to other global financial hubs like Singapore and Hong Kong, says a grouping of private bankers in Switzerland.
- There are also few deposits of Indian residents in Switzerland, as opposed to Singapore or Hong Kong for instance
- Official data: Money held by Indians in Swiss banks declined to a record low of 1.2 billion franc (about Rs 8,392 crore) at the end of 2015.
- Automatic exchange of tax information:
- Last week Switzerland ratified the decision to implement this regime with India and 40 other jurisdictions.
- The framework for automatic exchange of information requires strict adherence to data confidentiality, but the Geneva-based Association of Swiss Private Banks said it has no particular concern over India, where the rule of law seems to be properly upheld.
2. Secrecy must for automatic info exchange, Swiss banks tell India
Context: India recently signed automatic exchange window agreement with Switzerland.
In news:
- India will have to ensure strict confidentiality of information about its citizens’ Swiss bank accounts received through the new automatic exchange window, failing which the Alpine nation will stop sharing the data.
- Switzerland and its banks will also keep a close watch on the data protection measures taken by India regarding the details received from other jurisdictions and want all other global financial centres to implement the global framework for automatic exchange of information (AEOI) on financial matters.
- The pact with India is planned for implementation in 2018, with the first set of data to be exchanged in 2019.
The exchange of information would be based on the Multilateral Competent Authority Agreement (MCAA) on AEOI, which is in turn based on the international standard for the exchange of information developed by the Organisation for Economic Co-operation and Development (OECD).
D. GS4 Related
Nothing here for Today!! !
PIB Articles Editorials Roundup
E. Concepts-in-News: Related Concepts to Revise/Learn
Prelims worthy factual information
- NASA’s Orion spacecraft: designed to take astronauts to deep space destinations such as the Moon and Mars.
F. Bills/Acts/Schemes/Orgs in News
|
Scheme in News |
About the Scheme |
|
‘National Mission on Cultural Mapping of India’ |
Features of the scheme:
Key Point:
Main vision:
|
|
Articles in News |
About the Article |
|
Article 21 |
Protection of life and personal liberty No person shall be deprived of his life or personal liberty except according to procedure established by law. |


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Code Repository¶
The code repository is at github.com/ucscHexmap/hexagram, in the dev branch for development.
Repository branches¶
There are two main branches, “master” and “dev”. Master is used to hold the latest production version so should be kept clean. Nothing is ever comitted directly into the master branch. It gets updated by the repository meister when there is a new release by merging from the dev branch.
You may use personal or project branches off of dev however working directly on the dev branch is fine. Working directly on dev will allow the rest of us to use your changes as soon as you push them to the remote repository. Otherwise you will need to do a merge for others to easily use your work.
A git quick start¶
Git comes pre-installed on most systems. Otherwise see https://github.com to install it.
https://www.sourcetreeapp.com has a great UI for dealing with most of git. It does all of the commands below and is especially good for viewing diffs. However it is good to understand the sequence of events and commands behind it, and sometimes the UI is slow to update.
These commands are everything you need from the point of checking out the dev branch through committing your files and merging to dev if you’ve branched off of it. If things awry, you may need some other commands.
#1. Get a copy of the source code on the dev branch. Change to the directory where you want to put the source code, then:
git clone -b dev --single-branch https://github.com/ucscHexmap/hexagram
cd hexagram
#2. Get status to verify things went well and verify the branch:
git status
Now you can either work directly on the dev branch, or create your own branch off of dev.
Create your own branch if you want to isolate other developers from your changes as you save them to the remote repository. Then when you are ready to expose your changes to other developers, do a merge from your branch to dev. Your own branch is a good idea if you are working on something experimentally and you are not sure it will go into the common code.
Otherwise, working directly on the dev branch requires fewer merges and you just have to be more careful with each push to the remote. With fewer merges, this is an advantage if you are working closely with others on the same feature.
To work on your own branch create one as follows, otherwise skip this step and continue with the next. The commits, pushes and pulls in the following steps will apply to whichever branch your are currently on.
#3. We’ll call the new branch ‘mine’ for this example. Notice that to create a branch or change to an existing branch is the same command:
git checkout -b mine
git status
#4. Git has helpful messages when you want to commit. After you have added and changed files, ‘git status’ gives something like:
On branch dev
Your branch is up-to-date with 'origin/dev'.
Changes to be committed:
(use "git reset HEAD <file>..." to unstage)
modified: server/statsLayer.py
Changes not staged for commit:
(use "git add <file>..." to update what will be committed)
(use "git checkout -- <file>..." to discard changes in working directory)
modified: client/colors.js
Untracked files:
(use "git add <file>..." to include in what will be committed)
.server/myFile
Adding and checking in files is a two step process where files are staged before actually committed to the repository. In the above:
server/statsLayer.py is already staged for commit
client/colors.js is a modified, existing file
.server/myFile is a new file
So do the appropriate action to stage all the files you want to commit, then continue with the next step.
#5.  Add a comment and quit the editor. This commits files to your local git repository.
#6. If the commit went without any errors, you probably want to push it to the remote repository for safe keeping in case you lose the files on your laptop.
First pull down any changes from the remote repository so if a merge is required, you can do it locally rather than trying to fix up the remote repository where things could get ugly:
git pull
#7. If there are any merge conflicts, git will tell you about them, and after fixing and sanity checking, commit as in steps 4 & 5 above. If there are no conflicts, your repository now has any changes anyone else committed and pushed to the remote since last time you pulled. Now push your changes to the remote repository:
git push
Ta da! If you are working off the dev branch, you’re golden.
Merging from your branch into dev¶
If you are working on your own branch which is off of dev, you will eventually need to merge your branch into dev. We’ll use ‘mine’ as your own branch in this example.
#8. Change to the dev branch then update your local dev branch from the remote dev branch:
git checkout dev
git pull
#9. Now you do the merge from your branch to dev:
git merge mine
#10. Do sanity testing. Then push your dev to the remote dev:
git push
Releasing a new version¶
The release branch merges go like this, starting in the lower left corner:
.
#1. Check out the dev branch and update it.  Sanity test, update the remote master branch and create a release branch:
git push
git checkout v1.0_branch
#3. Change the version and cherry pick any changes you want in dev that were committed after the point of version branching:
vi mainHex.js # edit VERSION
git cherry-pick <list-of-commit-IDs>
#4. Sanity test, make fixes, tag, update the remote version branch:
git push
git tag v1.0
git push v1.0
#5. Merge the version branch into the master branch:
git checkout master
git merge v1.0_branch
git push
#6. Merge the master branch into dev:
git checkout dev
git merge master
git push
Some other handy git commands:
git branch -r
git ls-remote --tags


{% extends "layout_unbranded.html" %} {% block pageTitle %} Check your answers {% endblock %} {% block content %}
Sorry, we can't check you in as you're late for your appointment.
This doesn't mean your appointment has been cancelled.


Verificando...
Test offline app
Offline app
Test IndexedDB and Appcache for offline applications, sync when online.
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public class XMLUtilities extends XMLCharacters
| Modifier and Type | Field and Description |
|---|---|
static int |
IS_XML_10_NAME |
static int |
IS_XML_10_QNAME |
ALPHABETIC_CHARACTER, NAME_CHARACTER, NAME_FIRST_CHARACTER, NAME11_CHARACTER, NAME11_FIRST_CHARACTER, PUBLIC_ID_CHARACTER, VERSION_CHARACTER, XML_CHARACTER
| Modifier | Constructor and Description |
|---|---|
protected |
XMLUtilities()
This class does not need to be instantiated.
|
| Modifier and Type | Method and Description |
|---|---|
protected static java.io.Reader |
createXMLDeclarationReader(java.io.PushbackInputStream pbis,
java.lang.String enc)
Creates a reader from the given input stream and encoding.
|
static java.io.Reader |
createXMLDocumentReader(java.io.InputStream is)
Creates a Reader initialized to scan the characters in the given
XML document's InputStream.
|
static java.lang.String |
encodingToJavaEncoding(java.lang.String e,
java.lang.String de)
Converts the given standard encoding representation to the
corresponding Java encoding string.
|
protected static java.lang.String |
getXMLDeclarationEncoding(java.io.Reader r,
java.lang.String e)
Reads an XML declaration to get the encoding declaration value.
|
static boolean |
isXML11Character(int c)
Tests whether the given 32 bit character is a valid XML 1.1 character.
|
static boolean |
isXML11NameCharacter(char c)
Tests whether the given character is a valid XML 1.1 name character.
|
static boolean |
isXML11NameFirstCharacter(char c)
Tests whether the given character is usable as the
first character of an XML 1.1 name.
|
static boolean |
isXMLAlphabeticCharacter(char c)
Tests whether the given character is a valid aphabetic character.
|
static boolean |
isXMLCharacter(int c)
Tests whether the given 32 bits character is valid in XML documents.
|
static boolean |
isXMLNameCharacter(char c)
Tests whether the given character is a valid XML name character.
|
static boolean |
isXMLNameFirstCharacter(char c)
Tests whether the given character is usable as the
first character of an XML name.
|
static boolean |
isXMLPublicIdCharacter(char c)
Tests whether the given character is a valid XML public ID character.
|
static boolean |
isXMLSpace(char c)
Tests whether the given character is a valid space.
|
static boolean |
isXMLVersionCharacter(char c)
Tests whether the given character is a valid XML version character.
|
static int |
testXMLQName(java.lang.String s)
Test whether the given string is an XML 1.0 Name and/or QName.
|
public static final int IS_XML_10_NAME
public static final int IS_XML_10_QNAME
protected XMLUtilities()
public static boolean isXMLSpace(char c)
public static boolean isXMLNameFirstCharacter(char c)
public static boolean isXML11NameFirstCharacter(char c)
public static boolean isXMLNameCharacter(char c)
public static boolean isXML11NameCharacter(char c)
public static boolean isXMLCharacter(int c)
public static boolean isXML11Character(int c)
public static boolean isXMLPublicIdCharacter(char c)
public static boolean isXMLVersionCharacter(char c)
public static boolean isXMLAlphabeticCharacter(char c)
public static int testXMLQName(java.lang.String s)
IS_XML_10_NAME
and
IS_XML_10_QNAME
.public static java.io.Reader createXMLDocumentReader(java.io.InputStream is) throws java.io.IOException
is
- The input stream positionned at the beginning of an
XML document.java.io.IOException
protected static java.io.Reader createXMLDeclarationReader(java.io.PushbackInputStream pbis, java.lang.String enc) throws java.io.IOException
java.io.IOException
protected static java.lang.String getXMLDeclarationEncoding(java.io.Reader r, java.lang.String e) throws java.io.IOException
r
- a reader positioned just after '<?xm'.e
- the encoding to return by default or on error.java.io.IOException
public static java.lang.String encodingToJavaEncoding(java.lang.String e, java.lang.String de)
e
- the encoding string to convert.de
- the encoding string if no corresponding encoding was found.Copyright © 2022 Apache Software Foundation. All Rights Reserved.


Designs By TTOC Floral operates with the fundamental belief that our customers' needs are of the utmost importance. Our entire team is committed to meeting those needs.
As a result, a high percentage of our business is from repeat customers and referrals. We have over 25 years of floral experience and several certifications
in the industry. We welcome and look forward to the opportunity to earn your trust and deliver you the best service and designs idea in the industry.
Designs By TTOC Floral stands behind our guarantee that all of our flower arrangements, wedding décor and event decor will meet your standards. We are so committed
to making sure we can meet all of your floral needs.
~ Utilizes social media to engage with a community of fans/followers online
~ Coordinates online marketing and advertising campaigns
~ Collaborates with internal departments on projects and assignments
~ Demonstrates interest in social media and how media and communication strategies can continuously engage the online community
~ Provide links to 1-3 social networking profiles to demonstrate interest and knowledge
~ Possesses skills in writing, presentation, interpersonal relations, and customer management
~ Performs well in environment that values creativity, flexibility, and variety
~ Exhibits personal qualities, such as open-mindedness, enthusiasm, and adaptability
~ Prefers challenges, fast pace, new ideas, future focus, and unstructured environment
Paid.
July 29, 2016


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public abstract class DisplayInterface
extends java.lang.Object
implements java.io.Closeable
Display manager interface.
This class provides interface for switching between text and graphics display modes. It also provides interface for opening graphics framebuffer.
| Modifier and Type | Field and Description |
|---|---|
protected JavaFramebuffer |
fbInstance |
| Constructor and Description |
|---|
DisplayInterface() |
| Modifier and Type | Method and Description |
|---|---|
protected void |
closeFramebuffer()
Close the internal framebuffer.
|
protected void |
initializeFramebuffer(NativeFramebuffer backend,
boolean enable)
Initialize new internal instance of JavaFramebuffer.
|
abstract JavaFramebuffer |
openFramebuffer()
Get the framebuffer for the system display.
|
void |
releaseFramebuffer(JavaFramebuffer fb)
Remove all references to this framebuffer.
|
abstract void |
switchToGraphicsMode()
Switch the display to a graphics mode.
|
abstract void |
switchToTextMode()
Switch the display to a text mode.
|
protected JavaFramebuffer fbInstance
public abstract void switchToGraphicsMode()
Switch the display to a graphics mode.
java.lang.RuntimeException
- when the switch failspublic abstract void switchToTextMode()
Switch the display to a text mode.
java.lang.RuntimeException
- when the switch failspublic abstract JavaFramebuffer openFramebuffer()
Get the framebuffer for the system display.
The framebuffer is initialized only once, later calls return references to the same instance.
java.lang.RuntimeException
- when switch to graphics mode or the framebuffer initialization fails.public void releaseFramebuffer(JavaFramebuffer fb)
Remove all references to this framebuffer.
fb
- Framebuffer to remove.protected void closeFramebuffer()
protected void initializeFramebuffer(NativeFramebuffer backend, boolean enable)
backend
- Device behind JavaFramebuffer.enable
- Whether to enable framebuffer flushing from the beginning.


"PARVAIM "the name of a country from which Solomon obtained gold for the temple (2 Chronicles 3:6). Some have identified it with Ophir, but it is uncertain whether it is even the name of a place. It may simply, as some think, denote “Oriental regions.”
"PARVAIM "the name of a country from which Solomon obtained gold for the temple (2 Chronicles 3:6). Some have identified it with Ophir, but it is uncertain whether it is even the name of a place. It may simply, as some think, denote “Oriental regions.”


LA BELLE NOISEUSE ( director: Jacques Rivette; cast: Michel Piccoli (Frenhofer), Jane Birkin (Liz), Emmanuelle Beart (Marianne), David Bursztein (Nicolas), Gilles Arbona (Balthazar), Marianne Denicourt (Julienne), Marie Belloc (Magli), 1991-Fr.)
Rivette has created a work of art from a short Balzac story about art, "The Unfinished Masterpiece." Art and life are viewed as one and the same problem, in this film about a wealthy, once successful artist Frenhofer (Piccoli), as he searches for his sanity through his art, who is now troubled that he can only paint a masterpiece or nothing, and for the last 10- years the later was the result, except for some trivial self-portraits. His wife Liz (Birkin), who modeled for his former masterpiece, is concerned that something tangible has gone out of the marriage, though they are still a loving couple, blessed with a young daughter.
Frenhofer's art agent, Balthazar (Gilles), brings along a young struggling artist Nicolas (David), to visit the Frenhofer mansion at Languedoc. He is an admirer of Frenhofer's work and wishes to meet him. There is also the young artist's attractive live-in girlfriend Marianne (Emmanuelle), of the last three years, someone he met when he saved her from throwing herself in front of the metro. She writes children's books, but does not really consider herself a writer. It is just something she does so she could be independent of Nicolas.
The two artists intellectually engage in a discussion of what art means to them. But when Nicolas and Marianne are together, they try to picture themselves living in Freno's mansion, the place is so enormous and quiet, beyond what either of them says they are currently looking for in life; though he offers no comment about what he really thinks, while she openly disdains the place.
After being encouraged by a visit to Freno's atelier, a place he hasn't been to in two months, the guests view his paintings and warm up to their conversations with the host. The younger artist brashly states, "That for him, art is about taking risks, it is a bold stroke, something that stands out." Freno declares, "That art to him is when the forest and sea submerge as one." For Freno, "In order for the truth to come out of a work of art, there must be blood on the canvas."

La Belle Noiseuse, which we are told, is the title of the masterpiece, is about a 17th century lady of the world who was kind of nutty in the sense that she was difficult to figure out, who is referred to as being someone who is a "ball-buster."
With Freno back at work and the air filled with tension, you might as well say, let the games begin, and they do, but under Rivette's masterly direction what happens is what you might expect to happen but not in the way you expected it to happen, with the result being a fascinating look at how an artist tries to get at the essence of what he is doing, struggling with all the human emotions of passion and intellectualism, as those around him become in one way or another part of his work, as their jealousies, sexuality, and life ambitions come to the surface, in what transpires over the three day period he works with the nude model.
Every character has a part to play in the dynamics of the artist's creation, as he struggles to relate with his recalcitrant (she is steamed at Nicolas for not consulting her, saying "you sold my arse") and difficult model (this mansion reminds her of boarding school where she was sick all the time, until they eventually kicked her out of the school), as he finds that he must use his wits to get her to do what he wants her to do, because she is determined to be who she is, that is, until she becomes hypnotized under the artist's careful scrutiny and finds it impossible to wear the mask in life she has previously worn. The new question becomes, who is she now?
What makes for a captivating depiction of an artist at work, are scenes such as these, where one's sense of time is lost, and the length of the picture, (it is 240 minutes) does not seem wasted even for a minute, as we watch and become part of the creation, starting from scratch, and actually are hearing the artist's scratching sounds on the canvas for minutes at a time with no action on the screen but to view him work and watch him manipulate the model into the pose he wants, even when she complains that he is hurting her.
That the truth is cruel might have seemed like bullshit to her when Freno first said it, but now that Marianne is getting a grip on herself, she is no longer scared of all the tension that is in the studio and what is going on with her relationships-- that is, with Nicolas and Liz, as well as with the strange attraction she has for the 60ish and much older artist.
The girl-to-girl talks with Liz do not seem to do anything for her. She is just curious how Liz met the artist. And when told, they met in a cafe, and that he fell for her first before painting her, she seemed satisfied in knowing this but showed no concern of ever becoming a friend to Liz. Liz, on the other hand, is aware of what her husband is like, she knows he will behave properly with the model while working with her, she realizes that his work is everything, but she also knows there is a danger in these two working together, that sparks could fly, that he is looking for something in the model's beauty that he can no longer find in her; and that's what is upsetting to her, as she tries to play the role of supporter of her husband, by making sure Marianne feels reassured to continue modeling, yet guarded that something could go wrong that might upset her own relationship with Freno.
Marianne tells Freno that she is through with Nicolas, even though, he is the only man she can live with, she must move on. Nicolas is consumed with jealousy, admitting that it is he who needs Marianne now, not like the reverse situation when they first met. He wants her to stop modeling and return with him to Paris. She not only refuses, but she takes a guest room in the Frenhofer's, leaving him alone in the inn they were staying at.
Frenhofer is stuck. He is filled with self-doubt if he can ever paint again.
 She goes on to say, "I need to understand this"... It seems the situation has reached a point of no return. Every character is now playing out his emotional trump cards. The artists are struggling with what is not clear inside themselves, as their wounds are opened and their vulnerabilities seem to be devastating.
Liz tells her husband, "You are sad because you are no longer young, 10- years is a long time to stop painting and to now go on. You will only destroy what happened before you start over." There is a hint of a possible affair that might have taken place between Balthazar and her ten- years ago, that seems to be the cause of the tension we feel among the three of them.
In contrast to Freno, Nicolas can't stand the solitude, he is afraid to be alone with himself. When left alone, he takes comfort in the company of his sister (Denicourt), who joins him at the inn where he is staying.
Liz says, "for Freno, it is the art of it, it is the capturing of a whole life in a painting--- it is that thing that makes art shameless, that is what matters to him. It is as if one can see one's whole life passing in a flash, like it might be for a person drowning."
While discussing their relationship, Nicolas states to Frenhofer, "the only enemy of an artist is a bad painting." He gets his digs in by insulting the artist's lifestyle as comical. So the camaraderie between the two artists seems to be genuinely plausible, in the sense, that they do understand each other, that is, as far as their work goes. With Freno, in the position of control in his life, he is able to patronizingly say to Nicolas as he departs, " I like you, don't ever change."
The last shot is with the agent, talking numbers with Frenhofer, deciding how much they will get for the masterpiece. The implication being, as Balthazar invites Nicolas and his sister to dinner, that Nicolas is next in line, he will profit from his art in due time.
The acting is exceptionally good by everyone. Piccoli as the artist is mesmerizing, while Emmanuelle is both beautiful and intelligent, offering a special quality about her that makes it possible for us to believe that a masterpiece could come out of her poses. The only thing that struck me as odd, is that the final masterpiece drawn, supposedly by Bernard Dufour, did not appear to me to be a masterpiece, but a rather ordinary work. The picture itself is the masterpiece; that is, the creative process itself, was convincingly done, by a director who has the skills and knowledge to tell such a story and never allow the story to be wavering from its lofty position of significance, as anything but an honest intellectual effort, a search for the truth within.
REVIEWED ON 11/25/98 GRADE: A+
Dennis Schwartz: "Ozus' World Movie Reviews"
http://www.sover.net/~ozus
© ALL RIGHTS RESERVED DENNIS SCHWARTZ
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Federal judge says former White House counsel Don McGahn must speak to House
by CNN NewsourceA federal judge said Monday that former White House counsel Don McGahn must comply with a House subpoena.
"However busy or essential a presidential aide might be, and whatever their proximity to sensitive domestic and national-security projects, the President does not have the power to excuse him or her from taking an action that the law requires," the judge writes
This story is breaking and will be updated.


---
title: "Chinatown"
permalink: /chinatown/
---
Chinatown Revitalization
A century ago, Portland had the second largest Chinese population next to San Francisco. It once counted for 10% of population in Portland. Chinatown has been not only one of the prominent landmarks but a legacy for this city. Chinatown had its up and down in the past, but never lost its hope. With the new generation of Chinese immigrants moving into this city in the last 30 years, the Chinese community has pledged to work together to help revitalize Chinatown, to make it great again.
Portland Chinatown Chinese New Year Celebration
{% for gallery in site.chinatown_newyear %}
{{ gallery.title }}
{% endfor %}
Portland Chinatown Performance Photo Galleries
{% for gallery in site.chinatown_gallery %}
{{ gallery.title }}
{% endfor %}
Community Engagement in Chinatown
{% for gallery in site.chinatown_engage %}
{{ gallery.title }}
{% endfor %}
Wong Laundry Legacy in Chinatown
{% for gallery in site.chinatown_wonglaundry %}
{{ gallery.title }}
{% endfor %}