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My Computational Journal Summer 2012
Week 1
May 14, 2012
Today code for a simple ANOVA and a comparison of two strains was tested to see if the results produced by our adviser could be reproduced. The output without modifying the code for the comparison of two strains using wildtype and dGLN3 for the comparison could be reproduced. A few difficulties have been faced when trying to modify the simple ANOVA code. It was attempted to match the results produced for dGLN3 using the two strain comparison code with the results of the simple ANOVA code with the input specified as the log fold concentrations for the dGLN3 data. After being initially unsuccessful, the code was revisited and looked at more closely. It was found that two matrices in the matrix division had an unequal number of rows (matrix X and matrix Y). The indices (which specify columns of the input file) were modified after which matrix X had the same number of rows as matrix Y. The following code was used:
ind15 = ind15-indx(1)+1; ind30 = ind30-indx(1)+1; ind60 = ind60-indx(1)+1; ind90 = ind90-indx(1)+1; ind120 = ind120-indx(1)+1;
However, the results from the simple ANOVA for dGLN3 still did not match the results for dGLN3 from the comparison of two strains code.
Katrina Sherbina 21:31, 14 May 2012 (EDT)
May 15, 2012
A separate set of indices were made to designate the rows of the X matrices for the reduced and the full model. This separate set of indices (one for each timpeoint) removed rows of zeros that were previously added when substituting the select 0's for 1's to create the two X matrices. As a result, it was possible to call upon the original indices to extract the log fold changes corresponding to a specific deletion to create the Y matrix. After these corrections, the two strain comparisons were performed between wildtype and each one of the deletion strains.
Further modifications were made to the two strain comparison code to be able to make a comparison of all of the strains simulatenously. To do so, indices were added to designate the columns in the input corresponding to each of the deletion strains. A separate set of indices (one index per timepoint) for each strain as in the case of the two strain comparison. The parameters p were increased to 25 (five timepoints for each deletion strain) and the constraints q were increased to 20 to yield an X and Xh matrices with the appropriate numbers of columns. Changes were made to the out_data(ii,[number]) lines to account for the increase in the number of strains being compared. In the output, the data for each of the timepoints for each of the deletion strains matched the corresponding data in the two strain comparisons.
The next task is figure out how to handle missing data. Since both GCAT and Ontario chips were used, log fold change concentrations are missing for some genes for some timepoints for the wildtype (these cells show up as NaN). One possibility is to modify the X matrices so that they take into account the NaN's for each gene. On this note, a for loop was begun to try to exclude timepoints for a gene for which there is an NaN.
Katrina Sherbina 20:38, 15 May 2012 (EDT)
May 16, 2012
NaN's were removed from the Y matrix for each gene by using the command YY = Y(~isnan(Y(:,1)),1). This truncated the Y matrix from 43 rows to 34 rows. However, in doing so, it was not possible to solve for beta (the solution to the linear system XB=Y). Another method to deal with the NaN's was to replace them with a very large number using the command Y(isnan(Y(:,1)),1)=1e6 in order to be able to recognize the timepoints and flasks for which there were NaN's in the output. However, this messed up the B&H corrections.
The next step will build on trucating the Y matrix by getting rid of the rows with the NaN's altogether. To keep this step, the X and Xh matrix pairs must be formulated so that they are unique to each gene. A possibilty is to use a for loop to define each of the indices for each gene by the columns that do not contain an NaN for that gene. The Y matrix calculations would have to be within this loop.
Katrina Sherbina 21:33, 16 May 2012 (EDT)
May 17, 2012
A for loop was experimented with to generate different X and Xh matrix pairs for each gene to take into account those genes that have an NaN for a a flask for a timepoint in the wildtype. This loop contained a majority of the same coding that was used to set up the indices in the original two strain comparison code. The different lines of code are
for ii=1:n I = find(~isnan(a(ii,1:23))); ind15 = I(find(I>=1&I<=4)); ind30 = I(find(I>=5&I<=9)); ind60 = I(find(I>=10&I<=13)); ind90 = I(find(I>=14&I<=18)); ind120 = I(find(I>=19&I<=23));
indX = find(indx); end
These new lines of code retain the original column numbers of matrix a (the matrix containing the log fold change data) in the indices. The NaN's were then also removed from the corresponding Y vectors. At first, the loop to compute the Y matrix was put into the loop to compute the X and Xh pairs. However, the code ran for too long at that point. Then the Y loop was separated from the loop to compute the X and Xh matrices. An output was generated. However, for any of the genes that had at least one NaN, the entire row for that gene was blank. In dissecting this new code several problems were found. First, the X matrices for genes that had NaN's were not being computed correctly. Since the indices still had the original column numbers of matrix a, the ones were not put into the X matrix in the correct places. Briefly, cell arrays were looked at as a solution instead of numerical arrays because there can be blank cells in a cell array but numerical arrays do not contain blanks. However, this potential solution proved to complicate the calculations that need to be made.
May 18, 2012
(This entry is being written on May 20th regarding the work that was done on May 18th.)
The first issue that was tackled was the improper formation of the X and Xh matrices. For any of the genes that had at least one NaN, the 1's were put in the wrong positions in the X and Xh matrices. This is because the indices that were used to replace the 0's in the X and Xh matrices with 1 did not start at 1. This was necessary to later exlude the cells that had NaN's in the Y matrix. Rather than getting rid of the method to select the cells that do not have NaN's, the indices that were used to replace the 0's with 1's in the X and Xh matrices were renumbered if indx (the matrix of the indices for each time point) was less than 23 (the maximum number of columns correponding to the wildtype if none of the cells have an NaN for that gene). The following added bit of code was put into the for loop for the X and Xh matrices after the indx, indX, i1, and i2 lines of code:
if indx<23 ind15 = find(ind15); ind30 = ind30-ind15(end)+1; ind60 = ind60-ind30(1)-1; ind90 = ind90-ind60(1); ind120 = ind120-ind90(1); end
However, this may have fixed the X and Xh matrices. However, in the final output, the rows corresponding to the genes with NaN's were still completely blank.
At this point, the wrong direction was taken to find a solution to this. Some experimenting was done to produce X and Xh matrices all of which had 43 rows but some of which had something other than a 0 or 1 in the cell to designate the NaN in the original a matrix. Along this line, the NaN's were kept in the Y matrix. The goal was to be able to somehow ignore the NaN's then when calculating beta and betah.
It was considered to keep the NaN's because it was thought that the problems with the output had to do with some X, Xh, and Y matrices having less than 43 rows while others had 43 rows. Then looking back at how linear systems of equations are solved from what I learned in my linear algebra class, I realized that the number of rows could not be the reason why the some rows of genes in the output were completely blank. Even though the number of rows changed, the number of columns corresponding to the different type points never did. All the X matrices had 10 columns and all the Xh matrices had 5 columns. Therefore, there should be 5 betas being calculated (one for each timepoint) for the wildtype and for dGLN3 for all of the genes regardless of whether or not a gene had NaN's.
The next step in troubleshooting the code will be testing it with just a select number of genes that have NaN's for some timpeoints and flasks.
Katrina Sherbina 23:44, 20 May 2012 (EDT)
Week 2
May 21, 2012
The two strain comparison code was tested with an output that contained only seven genes (six of which had an NaN). At this point, there were no blank rows. To fix the blank rows that appear for genes with NaN's, the computation for the y loop was put in the same loop as the computations for the X and Xh matrices. This ensured that when the betas and betahswere being caluclated that the X and Xh matrices changed accordingly (depending on the gene for which the computation was being done). Previously, the code was set up so that he betas and betahs were calculated with the last X and Xh matrix that was computed in the loop.
Several changes were made to this code to compare all strains (wildtype, dCIN5, dGLN3, dHMO1, and dZAP1). First, indices were created for dCIN5, dGLN3, dHMO1, and dZAP1 (the two strain comparison code only had matrices for the widlytpe and dGLN3). The indices for the deletion strains were constructed for each timepoint similar to how they were constructed for dGLN3 making sure to specifiy the appropriate columns in the original data for each strain.
So that the X and Xh matrices were of the correct size and had 1's and 0's positions in the correct columns and rows, the indices for each timepoint for each strain were adjusted in the for loop.
i3 = ind1202m(end); i4 = indx3(1);
ind153m = ind153-i4+1+i3; ind303m = ind303-i4+1+i3; ind603m = ind603-i4+1+i3; ind903m = ind903-i4+1+i3; ind1203m = ind1203-i4+1+i3;
i5 = ind1203m(end); i6 = indx4(1);
ind154m = ind154-i6+1+i5; ind304m = ind304-i6+1+i5; ind604m = ind604-i6+1+i5; ind904m = ind904-i6+1+i5; ind1204m = ind1204-i6+1+i5;
i7 = ind1204m(end); i8 = indx5(1);
ind155m = ind155-i8+1+i7; ind305m = ind305-i8+1+i7; ind605m = ind605-i8+1+i7; ind905m = ind905-i8+1+i7; ind1205m = ind1205-i8+1+i7;
In addition, the the calculations for t, t2, and N were expanded to include all of the indices for all of the strains. The X and Xh matrix for genes with no NaN's had dimensions 103x25 and 103x5, respectively. The X and Xh matrices for the genes with NaN's had dimensions 94x25 and 94x5, respectively.
The coputation for the Y matrix was also altered to include all of the strains:
Y = [a(ii,indx)';a(ii,indx2)';a(ii,indx3)';a(ii,indx4)';a(ii,indx5)'];
The lines of code corresponding to the dimensions of the out_data were also altered to include all of the betas and betahs.
In addition, a few plots from the all strain comparison of the time versus expression genes with both low and high p values were saved. To do so, the if statement for the plots was removed. The save statement used to save each plot generated separately was
saveas(gcf,['Fig' num2str(ii) '.jpg'])
It would be beneficial to change this line of code so that the name of the figure corresponding to the gene for which the expression was being plotted.
Also, an avi file was made of the plots of time versus expression for genes with a p value of less than 0.05 and then those with less than 0.04 (this p value was observed to be the cut off for the B&H corrected p values in the final output for the all strian comparison). The plots for the genes with a p value less than 0.04 have to be redone because a banner that popped up in the figure window was also recorded (it blocks the gene name).
Before the for loop, the following line of code was added
aviobj = avifile('allstrain.avi','fps',15,'compression','Indeo3');
Some fiddling may still need to be done with the number of frames per second.
The following lines of code were added at the end of the for loop (after the if statement for to generate the plots):
%To get the handles from the figure open. Saves the entire figure window that is open. frame = getframe(gcf); %Adds the currently open plot to the avi file. aviobj = addframe(aviobj,frame);
Right after the for loop, a command line was added to close the avi file:
aviobj = close(aviobj);
The avi file had to be opened in QuickTime player. It would not open in windows media player when either the compression format was Indeo3 or Indeo5.
May 22, 2012
Some changes were made to the code to write an avi file. However, despite all of the revisions, the avi file was not being made properly. For the first few seconds the plots that showed up for some of the genes looked nothing like they should. To be able to even play the file, the compression had to be set to 'None'. This is what probably caused the file to be 4 GB. They appearance of the strange graphs at the beginning of the movie may be attributed to the large size of the file.
Initially, the p values showing up in the plots in the avi file did not match the p values for the corresponding genes in the output. However, this error was fixed by adjusting the if statement in the loop that creates the plots for genes with a p value of less than 0.05.
if pval<0.05 figure(1),plot(t,Y,'bo'),hold on,plot(t,Ym,'r+','LineWidth',3),plot(t,Yh,'k^','LineWidth',3), title([b{ii+1,1} ' W = ',num2str(W),' pval = ',num2str(pval)]),... xlabel('time, minutes'),ylabel('log fold change'),legend('data','model'),drawnow hold off nsig = nsig + 1; [ii,nsig] end
The rest of today was spent dissecting the code we currently have for the deterministic model. The goal is to split the code for the general parameter estimation function into multiple parts, namely, reading the files into matlab, the least squares error function, plotting the graphs, and writing the output.
Katrina Sherbina 20:38, 22 May 2012 (EDT)
May 23, 2012
The lines of code to create an avi file from the plots from the all strains comparison were fixed (thanks to Dr. Fitzpatrick). The changes include the following line of code before the for loop:
figure(1) set(gcf, 'DoubleBuffer','on'); yourMovieFileName = ['all_strain_comparison_p_value_less_than_0.05_Cinepak.avi'];
The frame = getframe(gcf) and aviobj = addframe(aviobj,frame) inside the if statement to generate the plots was removed. The aviobj=close(aviobj) line of code immediately after the for loop was replaced with
This time the movie generated with Cinepak compression code be played on Windows Media Player on an XP operating system. The size of this movie was significantly smaller than the size of the previous movie made without compression that could play with Windows Media Player.
There are three different scripts for the statistical analysis in MATLAB:
- all_strains_compare_movie.m to do a comparison for all strains
- wildtype_deletion_strain_compare.m to do a comparison between the wildtype and another strain
- two_deletion_strain_compare.m to do a comparison between two deletion strains
The two strain comparison code was divided into two (the scripts in the last two bullets above) because the for loop designed to remove NaN's is not necessary for the deletion strain data. The principle differences between these two scripts is the calculations to renumber the indices. The following is the part of the script for the wildtype to deletion strain comparisons that contains differences with the other two strain comparison script:
%These indices are changed depending on what deletion strain is being analyzed ind152 = [33,34,35,36]; ind302 = [37,38,39,40]; ind602 = [41,42,43,44]; ind902 = [45,46,47,48]; ind1202 = [49,50,51,52];
p = 10; q = 5;
alpha = 0.05; % significance level for the tests
n152 = length(ind152); n302 = length(ind302); n602 = length(ind602); n902 = length(ind902); n1202 = length(ind1202);
indx2 = [ind152,ind302,ind602,ind902,ind1202];
n = length(a(:,1));
out_data = zeros(n,12); nsig = 0;
for ii=1:n I = find(~isnan(a(ii,1:23))); ind15 = I(find(I>=1&I<=4)); ind30 = I(find(I>=5&I<=9)); ind60 = I(find(I>=10&I<=13)); ind90 = I(find(I>=14&I<=18)); ind120 = I(find(I>=19&I<=23)); indx = [ind15,ind30,ind60,ind90,ind120]; indX = find(indx); if length(indx)<23 ind15 = find(ind15); ind30 = ind30 - ind15(end); ind60 = ind60 - ind30(1) - 1; ind90 = ind90 - ind60(1); ind120 = ind120-ind90(1); end n15 = length(ind15); n30 = length(ind30); n60 = length(ind60); n90 = length(ind90); n120 = length(ind120); i1 = indX(end); i2 = indx2(1);
ind152m = ind152-i2+1+i1; ind302m = ind302-i2+1+i1; ind602m = ind602-i2+1+i1; ind902m = ind902-i2+1+i1; ind1202m = ind1202-i2+1+i1; t = [ones(n15,1)*15;ones(n30,1)*30;ones(n60,1)*60;ones(n90,1)*90;ones(n120,1)*120;... ones(n152,1)*15;ones(n302,1)*30;ones(n602,1)*60;ones(n902,1)*90;ones(n1202,1)*120];
t2 = [min(t):5:max(t)]'; N = length(indx)+length(indx2);
X = zeros(N,p); Xh = zeros(N,p-q);
Xh(ind15,1) = 1; Xh(ind30,2) = 1; Xh(ind60,3) = 1; Xh(ind90,4) = 1; Xh(ind120,5) = 1; Xh(ind152m,1) = 1; Xh(ind302m,2) = 1; Xh(ind602m,3) = 1; Xh(ind902m,4) = 1; Xh(ind1202m,5) = 1;
X(ind15,1) = 1; X(ind30,2) = 1; X(ind60,3) = 1; X(ind90,4) = 1; X(ind120,5) = 1; X(ind152m,6) = 1; X(ind302m,7) = 1; X(ind602m,8) = 1; X(ind902m,9) = 1; X(ind1202m,10) = 1; end
The calculations for the Y matrices, beta's, betah's, fstats, pvals, and plots are within the for loop. These are the same calculations in the deletion strain to deletion strain comparison script. These caluclations are the only ones in the for loop for the deletion strain to deletion strain comparison script. The following is a part of the deletion strain to deletion strain comparison script that contains differences in comparison to the previous script.
%These indices are changed depending on what deletion strain is being analyzed ind15 = [91,92,93,94]; ind30 = [95,96,97,98]; ind60 = [99,100,101,102]; ind90 = [103,104,105,106]; ind120 = [107,108,109,110];
ind152 = [120,121,122,123]; ind302 = [124,125,126,127]; ind602 = [128,129,130,131]; ind902 = [132,133,134,135]; ind1202 = [136,137,138,139];
p = 10; q = 5;
alpha = 0.05; % significance level for the tests
n15 = length(ind15); n30 = length(ind30); n60 = length(ind60); n90 = length(ind90); n120 = length(ind120); n152 = length(ind152); n302 = length(ind302); n602 = length(ind602); n902 = length(ind902); n1202 = length(ind1202);
indx = [ind15,ind30,ind60,ind90,ind120]; indX = find(indx); indx2 = [ind152,ind302,ind602,ind902,ind1202];
i0 = ind15(1); i1 = indX(end); i2 = indx2(1);
ind15m = find(ind15); ind30m = ind30-i0+1; ind60m = ind60-i0+1; ind90m = ind90-i0+1; ind120m = ind120-i0+1;
ind152m = ind152 -i2+1+i1; ind302m = ind302 -i2+1+i1; ind602m = ind602 -i2+1+i1; ind902m = ind902 -i2+1+i1; ind1202m = ind1202 -i2+1+i1;
t = [ones(n15,1)*15;ones(n30,1)*30;ones(n60,1)*60;ones(n90,1)*90;ones(n120,1)*120;... ones(n152,1)*15;ones(n302,1)*30;ones(n602,1)*60;ones(n902,1)*90;ones(n1202,1)*120];
t2 = [min(t):5:max(t)]';
N = length(indx)+length(indx2);
X = zeros(N,p); Xh = zeros(N,p-q);
Xh(ind15m,1) = 1; Xh(ind30m,2) = 1; Xh(ind60m,3) = 1; Xh(ind90m,4) = 1; Xh(ind120m,5) = 1; Xh(ind152m,1) = 1; Xh(ind302m,2) = 1; Xh(ind602m,3) = 1; Xh(ind902m,4) = 1; Xh(ind1202m,5) = 1;
X(ind15m,1) = 1; X(ind30m,2) = 1; X(ind60m,3) = 1; X(ind90m,4) = 1; X(ind120m,5) = 1; X(ind152m,6) = 1; X(ind302m,7) = 1; X(ind602m,8) = 1; X(ind902m,9) = 1; X(ind1202m,10) = 1;
n = length(a(:,1));
out_data = zeros(n,12);
nsig = 0;
The dimensions of the X and Xh matrices in this case stay the same for all genes.
The rest of today was spent continuing to make changes to the MATLAB script for the deterministic model. Nick succeeded in separating the general parameter estimation function into four parts:
- Input and labeling of the master sheet containing the network, log2 fold change concentrations for each strain, optimization parameters, production rates, degradation rates, network b's, and simulation times.
- The call for the general least squares error and optimization
- Generating graphs
- Creating the output
The input of the mastersheet in this script is different from that in the previous general parameter estimation function. In the actual input sheet, the log2 concentrations were divided into several sheets (one for each deletion strain) and inputted sheet by sheet into MATLAB. In addition, the log2 concentrations for each flask for each timepoint were inputted rather than the average log2 concentrations for each timepoint. Indicators for the timepoints, strain name, and strain index were added to the optimization parameters sheet. This required modifying the for loop for inputting the optimization parameters.
The next steps with the deterministic model include making some changes to the general least squares error script where the error = ((log2(x1) - d1).^2) line of code needs to be modified to take into account the replicates in the log fold change data for each timepoint for each strain.
Katrina Sherbina 21:22, 23 May 2012 (EDT)
May 24, 2012
In order to modify the error calculation in the general least squares error function (in MATLAB) to take into account the change from using average log fold changes for each timpepoint to using all of the data, several modifications were made to other scripts. (To make any of these changes, I first dissected the various functions to understand the various parts more.)
The log fold change data had to be imported separately for each strain (this modification was made earlier in the week):
[log2FC(1).d,TX1] = xlsread(input_file,'wt_log2FC'); [log2FC(2).d,TX1] = xlsread(input_file,'dCIN5_log2FC'); [log2FC(3).d,TX1] = xlsread(input_file,'dGLN3_log2FC'); [log2FC(4).d,TX1] = xlsread(input_file,'dHMO1_log2FC'); [log2FC(5).d,TX1] = xlsread(input_file,'dZAP1_log2FC');
Nevertheless, averages for each timepoint were later calculated for the purposes of later plotting standard deviations on the time versus log fold change plots.
The driver to detect active genes will be taken out. All of the genes in the network are considered active genes. The assignment of a number to each active gene was done with the detect active genes script. Now the active changes are "detected" in the matrices with the log fold change data:
active = find(log2FC(1).d(2:end,1));
This array is called for in the general network dynamic function. The ode45 function in matlab approximates a solution to the differential equation defined in the general network dynamic function.
Previously, the error was calculated using the model and the average log fold changes for each timepoint from the data. However, this error calculation needs to be changed so that the unaveraged log fold changes can be used. A preliminary equation that was experiment with was
myerror = ((log2(x1) - d1([1 5 10],:)).^2)+((log2(x1) - d1([2 6 11],:)).^2)+ ((log2(x1) - d1([3 7 12],:)).^2) +((log2(x1) - d1([4 8 13],:)).^2);
The problem here is that the equation does not take into account the last replicate for the t30 timepoint (because t30 has five replicates while the other timpeoints have four replicates).
Another concern is the actual data d and d1 that is being fed into the general least squares error function and other functions. For now, both d and d1 correspond to just the wildtype data. However, we will want to use the deletion strain data for the model as well.
Katrina Sherbina 21:29, 24 May 2012 (EDT)
May 25, 2012
The functions written in MATLAB for the deterministic model were modified to include all of the data (not just the average log fold changes for each timepoint) in the various calculations.
Modifications were made in the parameters script and the error calculation (now called errormat) in the general least quares error function. The following lines of code were added to the script:
% % The first row of the log2FC data indicating all of the replicate timepoints td = (log2FC(1).d(1,:)); % % Finds the indices in td that correspond to each timepoint in tspan. tindex(1).indx = find(td == tspan(1)); tindex(2).indx = find(td == tspan(2)); tindex(3).indx = find(td == tspan(3)); n_times = length(tspan); % % Log2FC data for the wildtype d = (log2FC(1).d(2:end,:))'; % % The average log2FC for each timepoint for each gene. means = zeros(length(log2FC(1).d(2:end,1)),n_times); for iT = 1:n_times means(:,iT) = mean(log2FC(1).d(2:end,tindex(iT).indx(1):tindex(iT).indx(end)),2); end
% % Standard deviations for each timepoint for each gene. Necessary for the graphs % % that will be produced. sigmas = zeros(length(log2FC(1).d(2:end,1)),n_times); for iT = 1:n_times sigmas(:,iT) = std(log2FC(1).d(2:end,tindex(iT).indx(1):tindex(iT).indx(end)),0,2); end
It is necessary to still find the standard deviations and the means to be able to produce graphs for each gene of the log fold change versus time with the upper and lower error bounds for each timepoint.
The error calculation in the general least squares error function was modified with the following lines of code:
errormat = 0; for iT = 1:length(tspan) for iF = 1:length(tindex(iT).indx) errormat = errormat+(log2(x1(iT,:))-d(tindex(iT).indx(iF),:)).^2; end end % This is the sum of all the errors L = sum(errormat(:));
In the general least squares error function, a modification was also made to the first figure produced (with the counter and lse_out). At first, all of the data (not the average log fold changes) was being used to specify the second subplot in the figure which fits the model to the data. When viewing the figure, the model was being fit to only three of the thirteen sets of data points in the second subplot. There were thriteen sets of data points (in columns) since there are thirteen columns in the data due to the replicates in each timepoint. Instead of using all of the data, the code to produce the subplots was modified to instead use the average log fold change for each timepoint:
if(100*round(counter/100)==counter) figure(1),subplot(211),plot(theta,'d'), title(['counter = ' num2str(counter) ' lseout = ' num2str(lse_out)]) subplot(212),plot(means','*'),hold on,plot(log2(x1)), hold off,pause(.1) end
The script specifying the plots for each gene of log fold change versus time was modified. The if else statement having to do with cssigflg was removed. This designation had to do with the concentration sigmas (standard deviations) inputted into MATLAB when they were still in the input excel spreadsheet. However, since the standard deviations are now being calculated in MATLAB, there is no need to determine the kind of the plot to be produced depending on the value of cssigflg. The following is the new code for the plots:
if igraph == 1 concd = 2.^d(:,active); error_up = (means(active,:)+1.96*sigmas); error_dn = (means(active,:)-1.96*sigmas); for ii=1:n_active_genes figure(ii+2),hold on plot(time,log2(model(:,ii)),td,d(:,active(ii)),'o',tspan,error_up(ii,:),'r+',tspan, error_dn(ii,:),'r+','LineWidth',3),axis([tmin tmax -3 3]) title(TX1{1+(ii),2},'FontSize',16) xlabel('Time (minutes)','FontSize',16) ylabel('Expression (log2 fold change)','FontSize',16) end end
The global statement at the top of each script or function was also changed due to the aforementioned changes:
global A prorate degrate active inactive tspan d wts b alpha lse_out penalty_out counter parms parmnames tindex means
Further work will need ot be done on the plots. In the plots for MAL33 and ZAP1, the upper error bounds are not shown. The y axis may not to be adjusted to be larger than [-3,3]. Also, the model for HAP5, the model goes beyond the error bounds for the t60 timepoint.
In the output excel spreadsheet, there are no log2 optimized concentrations nor network optimized B's for FHL1, SKO1, or SWI6.
In addition to dealing with the aforementioned concerns, we need to explore how to include the deletion strain data in the model.
Katrina Sherbina 20:23, 25 May 2012 (EDT)
Week 3
May 29, 2012
Copies were made of all of the functions and scripts in order to keep the original scripts that worked last week when making modifications to these scripts today. The ending _strains was added to each m file.
A line of code was added to the estimation driver that indicates the sheet with the data of the deletion strain for which the script is being run at a given time. Since the model is to be found for each one of the strains, it makes it easier in the long run just to import the data for the deletion strain that the code will be run for.
This change was made in the process of spending the day changing the general network dynamics function to be able to run the model for each of the deletion strains. It was necessary to delete the information in the weights matrix and the degradation rates array that corresponded to the gene that was deleted in the deletion strain of interest. One of the lines of code added, finds the index of the gene deleted in a given strain by matching it to the sheet number in the input corresponding to the log fold change data for the deletion strain. To be able to incorporate this line, the variables num and indices were added to the global command line.
When running the entire code, the first error come up was a mismatch of dimesnions in the line WXB = -W*zz+B which computes the exponent in part of the differential equation that is a sigmoid function. This error was due to the fact that B (which corresponds to b) had 18 rows while the other two arrays had 21. This occurred because b was being recomputed in the general least squares error function. As a result, the recomputed b was renamed to bb.
However, another error occurred at line 43 in the LSE_strains script. The matrix dimensions do not agree. It's uncertain why these errors are occuring because after comparing each line of code Nick and I seem to be using the same scripts.
More troubleshooting will be done tomorrow to address the newest error.
Katrina Sherbina 20:57, 29 May 2012 (EDT)


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When reading the article in the April 2011 Sky & Telescope by Brian Kloppenburg and Tom Pearson about photometry with digital cameras, I was reminded of an article I wrote 5 years ago entitled "Measuring Skyglow with Digital Cameras." (Click here to download the article in PDF form.)
The article is (to my admitedly biased taste) full of good ideas that aren't fully fleshed out. I was hoping that someone would take those ideas and run with them — bring them into a form that's usable by the average amateur. It hasn't happened, so I'm issuing the challenge again.In retrospect, I spent far too much time talking about point-and-shoot cameras and too little on digital SLRs, which are more suitable for this application. At the time, many point-and-shoot cameras still had the manual controls and sensitivity needed for scientific work, while DSLRs were the province of professional photographers and a few serious amateurs. These days, point-and-shoot cameras have become more automatic and les sensitive, and DSLRs have become cheap enough for many people to buy.
Why use DSLRs to measure skyglow when the Sky Quality Meter is so convenient and relatively cheap? Because the SQM measures only the zenith and can't cope with the horizon, where light pollution is at its worst — and most directional. The SQM would probably yield a number around magnitude 19.5 per square arcsecond for the sky at my astronomy club's observing field, hiding the fact that it's overwhelmingly bright to the southeast, in the direction of Boston, and almost tolerable to the northwest, as shown in my digital camera mosaic.
What more needs to be done? A lot! My mosaics are produced with lots of manual labor that could theoretically be made automatic — calibrating the measurement, determining the precise fields of the component frames by matching star fields, and stitching the mosaic together. Software exists to solve each one of these problems separately, but not all together. It's all a matter of computer-programming time — which I don't have. Any takers?

subset: commoncrawl


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GH6604, Reviewed March 2000
National statistics on the amount of child abuse and neglect are difficult to obtain because states use different definitions. Some states report only substantiated cases that have been verified according to state law. Other states report and combine both the number of substantiated and indicated cases. In indicated cases of abuse there is reason to suspect abuse or neglect, but less evidence to prove it.
In the United States it is estimated that for every 1,000 children, there were approximately 15 cases of substantiated abuse and neglect. Missouri's rate of 15 cases per 1,000 children mirrors the national figure.
There are five general categories of child maltreatment:
Each of these includes a list of behaviors in its definition. Physical abuse includes scalding, beating or severe physical punishment. Sexual abuse includes incest, sexual assault, fondling of genital areas, exposure to indecent acts or involvement in sexual pornography. Emotional abuse includes verbal abuse and belittlement, terrorizing acts, and lack of nurturance or emotional support. Neglect occurs when a parent/care giver fails to meet the child's educational, supervisory, and medical needs. The "other" category includes abandonment, prenatal exposure to alcohol and other drugs, and threats to harm the child.
Often a child has been the victim of more than one type of abuse. Many children who are known to have been physically abused or neglected have also been sexually abused. Such sexual abuse may or may not be reported.
Researchers no longer believe that it is only the poor mental health of the parent or care giver that causes child abuse and neglect. Other factors that may be involved include financial stress and poverty, adult use of alcohol and other drugs, a lack of parenting skills and basic knowledge of child development, and the community and family in which the child lives.
Adults abuse children in different ways. For example, physical abusers tend to be lonely, angry, anxious and unable to make and keep close relationships with family members and friends. Neglectful adults, on the other hand, seem to be immature and unable to make life decisions about marriage, employment or having children.
The number of children who are abused and neglected will not decline without major efforts by federal, state and local officials to:
The following types of programs have been shown to have a positive effect on preventing child abuse and neglect:
If you witness or suspect that a child is a victim of maltreatment you must help. There are various programs in Missouri that offer assistance to both parents and children who are in violent situations. Reports of abuse should be made by telephone to the state's toll free hotline number (800-392-3738), county police departments or welfare offices as soon as possible.
Mandated reporters are individuals who have direct contact and supervision or care of children Ñ they are required by law to report instances of abuse. Examples of mandated reporters include, but are not limited to, teachers, child care workers, medical personnel, dentists, social workers and law enforcement. Mandated reporters are responsible for reporting abuse or neglect when there is reasonable cause to suspect that a child has been the victim of maltreatment. Mandated reporters must make a report when they suspect a child has been or may be subjected to conditions or circumstances which would reasonably result in abuse of neglect.
If you voluntarily report an instance of abuse, your identity will be kept confidential. However, you will be asked to give information on how you may be contacted if further investigation is needed. Your name will not be revealed as reporter of the incident of maltreatment.
Calls to the hotline should be made as soon as possible when abuse/neglect or maltreatment is witnessed or suspected. In order for the hotline to accept a report, it is important for the reporter to know the identity of the child, parents and the alleged perpetrator, and where the child can be located. There must be specific allegations of abuse or neglect, and the alleged perpetrator must have care, custody and control of the child. Other questions which will be asked by staff from the hotline include:
These numbers are available to assist you in your efforts to report cases of abuse and neglect:
In Missouri800-552-8522
Our staff can provide you with materials about reporting, how to help the victim, and other related topics.
We can provide support for the caller, problem-solve relationship, safety, communication, boundaries and other issues.
We can refer you to counseling services and transfer you to a child abuse hotlines directly if appropriate.
Order publications online at http://extension.missouri.edu/explore/shop/ or call toll-free 800-292-0969.


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This was supposed to hurt. Hurt like hell. Hurt like trying to pass a kidney stone the size of a croquet ball.
Six months of uninterrupted discomfort bordering on agony. Morphine, not patience, the only prescribed medicine capable of dulling the pain.
Instead, it's been the most fun in years.
Another unexpected perk Monday at the Scotiabank Saddledome, a 2-1 shootout win over a team they have absolutely no business beating, the 100-point San Jose Sharks.
If ever there was a piece of footage of what the "rebuilding" Calgary Flames are trying to sell, it was there for the posting at roughly 8:40 p.m. Monday. There was rookie defenceman Tyler Wotherspoon, a draft pick of all things, laying a beautiful cross-seam, 40-foot slap-pass on the stick of Joe Colborne, a local kid who actually wants to be here and bleeds the colours, for a roof job to begin another (ho hum) comeback.
Youth. Potential. Precision.
Their advertising dream.
Think about it . . . in the past two weeks, a comprehensive thumping of the championship-designed Ducks, Friday's wild 'n woolly 11-goal near comeback against Nashville, that cup-runneth-over 8-1 desecration of the Oilers (full of water-bottle splattering and jersey tossing and northern navel-gazing) capped off by a taut victory over another of those California powerhouses.
No, they're nowhere near a playoff spot.
Admit it, though, this dismissed rabble is starting to grow on you. If only just a little bit ...
Instead of languishing in 30th, where we simply assumed they'd eventually settle, they've already put the Buffalo Sabres, Oilers, Florida Panthers and New York Islanders behind them, in the shade. With the Ottawa Senators — anointed by a preposterous number of analysts as Canada's most tangible title hope at the start of the season! — Carolina Hurricanes and Nashville Predators still very much within range.
Which may not do wonders for draft positioning but is undeniably balm for the soul.
It all starts with Bob (The Rebuilder) Hartley. Like one of those guys you occasionally hear tell of who has crafted a life-size Eiffel Tower out of matchsticks or an Obama likeness out of chewing gum, he's taken ordinary, everyday, run-of-the-mill things — kids and castoffs, mostly — and fashioned more out of them than anyone believed possible, remaining so upbeat, even through the tortuous times, that concerned media wondered whether a physician shouldn't be summoned, or maybe a shrink.
Consider this: 43 of the Flames' 72 games have been decided by one goal. That, over and above any single statistic, more even than wins and losses, illustrates how shockingly competitive this group has become. They pushed past a disastrous stretch from the end of December through mid-January, losing nine of 11 while being blanked five times, to get back to their resilient ways.
Off what he's mined out of what he has, Hartley, by turns cajoling and coercing, doesn't merely deserve a contract extension but some kind of commemorative sash presented by Mayor Nenshi, the traditional western-themed bronze and free burgers at Peters' Drive-In for life.
It's actually unthinkable to conceive of anyone else being given the task of moving this project forward now, regardless of 'interim' GM Brian Burke's fondness for the unemployed Ron Wilson, or the currently-hanging-by-a-thread Randy Carlyle.
These Flames are indeed limited, but their buy-in has been limitless. And for that, Hartley deserves a deep bow.
From Mikael Backlund's emergence as an authentic two-way NHL centreman to the inspired, if obvious, choice of Mark Giordano as captain. From the hints being dropped by Karri Ramo that a successor to Miikka the Magnificent may actually already reside within the organization to liking what they've seen from Paul Byron, Tyler Wotherspoon, Markus Granlund and Lance Bouma. From the Boring Sean Monahan twitter account to Sean Monahan himself.
Most of it has to rank as a pleasant surprise.
The franchise low for points in a full-blown, 82-game season is 67, suffered in 1997-98. A lot of us, glancing down that wafer-thin lineup with an involuntary shudder in late September, figured this edition would be in with a legitimate shout at breaking it. Well, with 10 games still to go, they nudged the 67 plateau Monday night.
So there.
Wednesday, the Ducks, sure to be smarting from that hiding a week ago, are back. There'll be a buzz around the rink. And not just to see Ryan Getzlaf, Corey Perry and Teemu Selanne, either.
The post-season in a deep, strong, unforgiving Western Conference remains a ways, maybe even years, off. That's invariably the way of the rebuild world.
But at least they're pointed in the right direction now, and showing signs of life.
"It's an exciting time for us," skipper Giordano was saying late Monday morning, hours before another giant was slain. "I don't know what they perception is from the outside, but in here we think we're close."
'Close', of course, is a relative term.
But 'closer', yes that, certainly, than anyone of sound mind could've imagined.
George Johnson is the Herald's sports columnist. E-mail him at email@example.com
Follow George Johnson on Twitter/GeorgejohnsonCH


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The following hotels, B&Bs and holiday accommodation are located within 10 miles of AB301QR, ordered by distance from postcode:
Alternatively, use the search form to search for some great local deals on hotel rooms around Aberdeen.
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In the beautiful Scottish village of Edzell, boasting a sauna, a gym and a swimming pool, this hotel is situated at the foot of the Angus Glens. Guests at Glenesk Hotel can enjoy free WiFi and free parking on site.
Located in the beautiful small village of Edzell, The Panmure Arms Hotel offers bed and breakfast accommodation, a restaurant and free WiFi. The hotel is 40 miles away from Aberdeen and Dundee, and 10 miles from Montrose and the rail station.
Townhead Bed & Breakfast offers accommodation in Brechin. Free private parking is available on site. Every room has a flat-screen TV.
Founded as a coaching inn in the early 19th century, this charming 3-star hotel is situated in the ancient city of Brechin and now offers high-standard en suite accommodation.
Situated in the centre of Brechin, this traditional sandstone villa boasts free Wi-Fi and free parking. Gramarcy House is 8 miles from the seaside resort of Montrose, which features the sandy Blue Flag Montrose Beach.
Hillside Hotel is located in Hillside, around 3 miles from Montrose' seafront. This homely property features a restaurant and bar. The traditional rooms at Hillside Hotel is finished in pleasant pastel tones.
Situated in scenic Fettercairn, in the heart of Kincardineshire, Ramsay Arms Hotel features a traditional restaurant and bar. With free parking, the hotel also offers cosy rooms and free Wi-Fi.
The Cottage is a holiday home situated in Saint Cyrus, 47 km from Aberdeen. The property features views of the garden and is 48 km from Dundee. The unit equipped with a kitchen with an oven and toaster.
5 Milnamair offers accommodation in Montrose, 42 km from Dundee and 47 km from St Andrews. The unit is 31 km from Stonehaven. The kitchen comes with an oven and a toaster and there is a private bathroom.


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Feb 22, 2013 at 11:03 pm
Thanks man. I like your garage. I think your firehawk is cool.I bought an 02 firehawk conv yesterday.should be in my garage(feature) soon. are you going on bandit run 2013?
Feb 18, 2009 at 5:31 pm
Jan 19, 2009 at 10:14 am
DAMN!!! Nice cars my Fave would have to be the Redhead. Jesus u didn't think that thing had enough horsepower you had SUPERCHARGE it.


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When your partner or friend wakes up in the morning to discover a Cajun Steamer was delivered to them while they slept.
My roommate john was acting like such a jerk at the party last night we all decided after he passed out he deserved to wake up to a nice cajun sunrise compliments of they guy who just finished work at the mexican restaurant that night.
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Veteran offensive lineman Richie Incognito spent Tuesday with the Denver Broncos, a team searching for the right combination in the face of multiple injuries.
Reports claimed Incognito worked out for the Broncos and that the meeting was productive, but that he left Denver without a contract offer.
With running back Ronnie Hillman (foot) out at least two weeks and right tackle Paul Cornick (shoulder) likely to sit for the second consecutive game, quarterback Peyton Manning could have multiple players in new positions against the St. Louis Rams this week.
Incognito was a Pro Bowl guard with the Dolphins but could play right tackle. He has not played since he was...


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To celebrate this very special day, let's learn an awesome new flower design called Sunflower:
Inspiration - I love to play with flower designs, especially finding easier ways to create them without as much precise travel stitching.
One morning I was doodling and created a very simple flower, but all the petals were different sizes and it didn't look good. In frustration, I just kept adding more and more petals on top until the first set no longer looked bad. That's a great way to hide mistakes: cover them in a sea of flower petals!
Difficulty Level - Beginner. Sunflower is a super simple design and what's great is it will help you master creating a smooth petal shape. If you're struggling to make smooth shapes without wobbly lines, try quilting this design in some small blocks to practice
By the time you get finished, you'll have gotten a better handle on making these shapes, and created a nice stack of drink coasters as well!
Design Family - Center Fill. This design starts in the center of your quilting space and radiates out. Don't worry about the flower petals completely filling every corner of your blocks. It actually looks better if you keep the flower shape circular rather than trying to stretch the petals into a square.
Directional Texture - Center Focused. You really can't miss this eye catching design! If you watched the video, you'll have seen me go around the center one more time before I finished the design. I like building up my threads to really draw attention to the center of the design.
Suggestions for Use - I have a large quantity of small blue and white quilts left over from writing about How to Piece Perfect Quilts two years ago. All they need are some simple designs to finish them off to make many nice baby quilts. Sunflower would be a perfect design to use in the blocks and cornerstones!
Back of Sunflower
and make sure to tell your friends where you learned it.
Click here to support the project by visiting our online quilt shop.
Click here to support the project by visiting our online quilt shop.
Let's go Quilt!


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Featured News - Current News - Archived News - News Categories
by Kathy Duff
"So many families are struggling with hopelessness and despair," stated Mike Chorey, a native to Grand Island who is a pastor at Cross River Church in Niagara Falls. Chorey was speaking about the impetus for a Gospel crusade, the "Field of Miracles: The Return," which will come to Sal Maglie Stadium for three days in August.
The program includes music, Bible teaching and healing services, all geared to a multi-generational, God-centered message of hope.
Chorey has long had a vision for an "old fashioned, Holy Ghost-filled evangelistic crusade" in Niagara Falls and surrounding communities. The theme of the event (taken from Old Testament scripture) says it all: "Return to me, and I will return to you," said Chorey, who anticipates many individuals "coming to the cross of Jesus Christ for salvation and healing."
Chorey put together a similar "Field of Miracles" in Rochester some years back. The 2013 version in Niagara Falls has been seven years in planning. Chorey emphasized that, while the crusade is in Niagara Falls, he hopes to see families from surrounding communities attending the event.
The three-day lineup includes nationally recognized evangelist Jimmy Swaggart and his grandson, Gabriel Swaggart. The senior Swaggart began a television ministry in the '70s, which continues to air all over the world. Grandson Gabriel Swaggart is the youth pastor of Family Worship Center Church in Baton Rouge, La., and the head of CrossFire Youth Ministries.
Chorey sees "Field of Miracles: The Return" as "three days to come together to fellowship with Jesus Christ. God calls us His friends."
In addition, Bob Cornell of World Evangelism Bible College in Baton Rouge will present a seminar called "How to Live the Victorious Christian Life." The seminar on Saturday, Aug. 10, is free of charge, but will be at a separate venue - the Niagara Falls High School Performing Arts Center.
The events at Sal Maglie Stadium will take place at 7 p.m. on Friday, Aug. 9, and on Saturday, Aug. 10. The Sunday service starts at 6 p.m. Parking is free around the ballpark, and free shuttle buses will travel between the stadium and overflow parking at Niagara Falls High School on Porter Road.
For more information about "Field of Miracles: The Return," visit www.fieldofmiracles.org.
All three days are free of charge. A free-will offering will be provided for donations. Promotional materials for interested churches and organizations are also available at the website, or by calling 716-284-8173.
Sal Maglie Stadium is located at 1200 Hyde Park Blvd., in Niagara Falls.


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Deserts—What and Where
by Sarah Canzoneri
The Sahara is the world's largest hot desert. A desert is an area that is very dry. Any region that usually gets less than ten inches of precipitation (rain or snow) a year is a desert. Ten inches a year is not much: New York City gets about 42 inches a year; Orlando, Florida, gets 51 inches. Some deserts get no rain at all for years at a time.
Many people think that deserts are always hot and sandy, but they are not. Antarctica is a polar desert. Even larger than the Sahara, it is cold and has no sand at all—only ice and snow. Some deserts are hot in the day and cold at night. In the Sahara, the temperature can be 120°F during the day and 20°F at night. Some deserts have seasons with cold winter days and nights.
About one third of the land on Earth is desert, and there are deserts all over the world. Earth isn't the only planet with deserts. All of Mars is a desert, and Venus may have deserts, too.
Desert Extremes
- World's driest desert: The Atacama
- World's oldest desert: The Namib
- World's largest hot desert: The Sahara
- World's largest sand dune area: The Empty Quarter
- World's largest polar desert: Antarctica
- World's lowest spot: In the Negev Desert
- World's highest temperature: In the eastern Sahara
- What are the characteristics of a desert habitat?
[anno: A desert is an area that is very dry and gets less than ten inches of rain per year.]
- What kind of adaptations might an animal need to survive in the Sahara desert?
[anno: Answers may vary but could include that an animal would need to be able to stay cool during the day and warm at night.]
- If Antarctica is covered with ice and snow, why do you think it is considered a desert? Write a sentence or two to explain your answer.
[anno: It is a desert because it probably does not get very much precipitation each year. The snow and ice that are there have accumulated over time.]


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Jessica Chastain's nose
Here are some photos of Jessica Chastain leaving Venice and then arriving at Heathrow today. I'd like to talk about her nose. I've just realised how much I love her nose. If you've been reading this blog a while, you'll know that I have a nose fetish because of how I feel about my own nose. Which is a hawk nose. There's bump on the bridge so it slopes slightly downwards. I get it from my ma, the Chinese Squawking Chicken who, naturally, thinks her nose is wonderful. There obviously was no way I could ever change my nose. And besides, changing noses f-cks with face mapping feng shui. I'd rather have an ugly nose than bad feng shui. So I admire noses from afar.
Jessica Chastain's nose is so great.
It's so straight.
It's a strong long nose. It's a nose that isn't meek. It isn't overly aggressive. It's beautiful in profile. It's perfect.
La Pira / Brussa/ Splash


text:
Modular Building Institute USA holds its European Council Meeting at TUM br2
REbuild 2017 | Intervista a Thomas Bock - Baurealisierung und Baurobotik TU Munich
Mr. Ituralde presented the EU BERTIM Project at ISARC 2018 in Berlin.
Dr Barhye Ilhan presented EU Project BERTIM in Japan
Chairholder delivers Keynote on Strategic Research Programme for Robotics at Cities of Tommorrow Summit Singapore
Mr Wen Pan and Mr Rongbo Hu presented their scientific papers at the Creative Construction Conference (CCC) 2018 in Ljubljana, Slovenia
br2 Organizes 2 Missions from Hongkong Science and Technology Park and Construction Industry Council to Europe(Finland and Germany) on Automation and Robotics in Infrastructure and Modular Industrialized Building for Affordable Housing
Chair facilitates start-up creation in the field of construction robotics
Chairholder invited to university hospital geneva to talk on: The Robotic Future of Elderly Care
New CIB Proceedings W119-TG93: International Conference on Smart, Sustainable and Sensuous Settlements Transformation (3SSettlements)
The chair's BMBF project on "assistive workplaces" covered in ZDF's TV documentation series "plan b"
11th World Conference on Gerontechnology
Prof. Inaba of University of Tokyo gives a Talk on humanoid robotics at br2
Opening "Grieserhof" Carehome with LISA-br2-Moduls
BaltSe@nioR at Milan Design Week 2018
Guest Professor Dr-Ing. habil Alexej Bulgakov holds keynote speech at annual assembly of russian academy of architecture, city planning and construction sciences in moscow on 20th april 2018
br2 paper "A framework of indicators for assessing construction automation and robotics in the sustainability context" published in Journal of Cleaner Production
Japan based, multinational firm Kobe Steel (KOBELCO) visited br2 chair at TUM
Cover Page of White Book on Healthy Aging for Taiwan
Work anniversary Lecture Dr. Linner
Guest Professor Dr-Ing. habil Alexej Bulgakov holds keynote speech at annual assembly of russian academy of architecture, city planning and construction sciences in moscow on 20th april 2018
About us
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text:
'Imiloa Fulldome Film Festival
September 5 to 7, 2013
Mahalo to our 'Imiloa Fulldome Film Festival sponsors
"A Passion for Fulldome – IMERSA's Vision" Saturday, September 7 at 11:00am
Event registration and pricing
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"We are very excited to host the international fulldome film festival in Hilo," says Shawn Laatsch planetarium manager, "this will showcase the passion and artistry of the digital technology in the planetarium industry."
The festival is a unique chance for planetarium and museum professionals from around the world to preview and evaluate the latest content available for digital planetarium theaters. It will showcase a variety of production types including CGI (computer generated imagery), time-lapse photography, and full dome videography.


text:
Difference between revisions of "LinuxSampler"
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$ linuxsampler
$ linuxsampler
then {{
then {{|Ctrl+c}} to quit.
==== The editor : Gigedit ====
==== The editor : Gigedit ====
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* Let's define some audio outputs in qsampler :
* Let's define some audio outputs in qsampler :
:Go to menu -> View -> Devices (or {{
:Go to menu -> View -> Devices (or {{|F11}} shortcut or the green pci card icon in the toolbar).
:On the left panel, click on "Audio Devices".Now we can see the audio drivers available in the right panel.
:On the left panel, click on "Audio Devices".Now we can see the audio drivers available in the right panel.
:Choose "Jack" in the Driver menu.The default config should give you a pair of audio outputs at a sample rate of 44100.
:Choose "Jack" in the Driver menu.The default config should give you a pair of audio outputs at a sample rate of 44100.
Revision as of 10:44, 1 September 2013
- 1 Overview
- 2 Quick Installation
- 3 The (not so) long way
- 4 Advanced topics
- 5 Troubleshooting
- 6 External Resources
Linuxsampler is a software audio sampler.It can be loaded with sound libraries in the gigasampler format (.gig). One benefit of LS is it can stream the samples directly from hard disk, allowing the usage of huge libraries (several GBs..).LS can be started as a standalone application or lv2 or dssi plugin.Currently only the cvs build will provide those plugin versions. By now, "Linuxsampler" refers to a group of software interacting together :
- the sampler engine itself : linuxsampler
- a gig file editor : gigedit
- several graphical frontends : qsampler (QT based), jsampler-classic and jsampler-fantasia (both java based)
Quick Installation
All packages are available from the AUR.You have choice between release or cvs versions. If you choose the release versions then the most simple way is installing a frontend via yaourt, which will cascade all necessary dependencies in the right order :
$ yaourt -S qsampler
This should build and install in this order : libgig, linuxsampler, liblscp and finally qsampler. You could install jsampler instead of qsampler if you prefer this interface, or install it later. It's perfectly ok to have multiple frontends for LS in the system.
If you need the gig file editor :
$ yaourt -S gigedit
You can now run qsampler which will automatically start linuxsampler. If you use jsampler, you have to start linuxsampler first.
The (not so) long way
IMPORTANT NOTE 1 : Follow the installation order of theses components to get a working set of apps. All packages are available from the AUR. You have choice between release or cvs versions.
You should choose between a full set of standard packages OR CVS packages but do not mix them. Whatever you choose, but particularly with cvs packages, you should keep in a safe place a set of binary packages that work together.
The backend : Linuxsampler
It is the "engine" of the sampler, which performs all the heavy and time critical computational tasks of handling MIDI events, calculating the audio data and sending the final audio data to your sound card(s). LinuxSampler itself usually runs as own process in the background of the computer and usually does not show up anything on the screen, or at most it can be launched to show status information and debug messages in a console window. Usually you will also need a frontend to control it.
- Build and install libgig-svnAUR or libgig-cvsAUR
- Build and install linuxsampler-svnAUR or linuxsampler-cvsAUR
and check that the backend is ok :
$ linuxsampler
Ctrl+c to quit.
The editor : Gigedit
Gigedit allows you to edit and create instruments for the Gigasampler format, which can be used with LinuxSampler as well as with Tascam's Gigastudio. You can use gigedit as stand-alone application without Linuxsampler running or in live-mode, started from any frontend ("edit" button).In this case, all your modifications are audible in realtime.
- Build and install (optional, you can skip this step if you do not need the editor): gigedit-svnAUR or gigedit-cvsAUR
and check that everything is ok :
$ gigedit
The editor should pop-up in "stand-alone" mode as indicated in the down-right corner. Close the window.
The frontend : Qsampler
This frontend provides the user a set of menus, buttons, sliders, dials, etc. to allow the user to control the sampler in a convenient way. It does not perform any signal processing tasks, so you can see it as a "face" of the sampler. From Qsampler you can load/unload .gig files into Linuxsampler and set their midi channel number, volume, jack output etc...and finally store all this setup in a file for a speedy re-opening of your "sampling orchestra".
- Build and install : liblscpAUR or liblscp-cvsAUR
- Build and install : qsamplerAUR or qsampler-svnAUR
Building a default template in qsampler
Here, I will use jack-keyboardAUR as a MIDI controller, but everything below applies as well with a master keyboard or MIDI interface providing midi output.
- Start jack then jack-keyboard then qsampler
- Let's define some audio outputs in qsampler :
- Go to menu -> View -> Devices (or
F11shortcut or the green pci card icon in the toolbar).
- On the left panel, click on "Audio Devices".Now we can see the audio drivers available in the right panel.
- Choose "Jack" in the Driver menu.The default config should give you a pair of audio outputs at a sample rate of 44100.
- Click on the Create button down the window.
Note : In some systems, qsampler crashes if this window is closed or even backgrounded while the Bottom-Right panel is still in view.Easy workaround : click on "Audio devices" or "Midi Devices" on the left panel before leaving or unfocusing the window.
- If you want LS to auto-connect to jack system outputs when you launch your template :
- On the left panel, click on "Audio Jack Device 0" , then on right panel select "Audio Jack 0" from the "Channel" drop-down list.
- Choose an output for the JACK_BINDINGS parameter, like "system:playback 1".
- Select "Audio Jack 1" from the "Channel" drop-down list and assign JACK_BINDINGS parameter value, like system:playback 2"
- Now let's create a midi input also :
- On the left panel, click on "Midi Devices".
- On the right panel, choose "jack" (jack-midi) in the Driver menu.
- Hit the create button.
- If you want LS to auto-connect to jack-keyboard midi output when you launch your template :
- Select the "Midi jack device" port 0" on the left panel.
- On the right panel, for the "JACK_BINDINGS" parameter value, choose "jack-keyboard:midi out".
Note that if jack-midi is not enabled in Qjackctl, you won't find the midi client in the drop-down list.You can check in Qjackctl setup : "Midi driver" should be set to "seq".A restart of jack and qsampler is needed.
Also, if jack-keyboard or whatever midi controller you defined in here is not started before qsampler starts, you will likely receive an error from qsampler not finding the midi client.In that case, you can still start the midi device and connect it to LS through qjackctl.
- Finally close the Devices Config window and save your template.
Building a performance template in qsampler
- Open qsampler and load your configuration template.
- Press the "Add channel" button in the toolbar (Ctrl-A).A "channel" in the LS terminology is an object (visually a strip) which stores the settings for a given instrument : Name and location of the gig file, inputs & outputs used, midi channel, volume, solo/mute status, midi cc applied etc..much like a track in a sequencer.
- The i/o settings of the channel pops up.
- Choose a gig file
- Choose an "instrument".A gig file can contain different "instruments".Basically a gig file is composed of a pool of sounds and some configuration possibilities of theses samples named "instruments". For example one instrument can load only the forte samples and apply some adsr on it, while another one can load every samples in the pool, and organize them as layers that will be triggered by the velocity applied on the controller. This way, very different types of of sound can be obtained from the same pool of samples, which is more efficient in terms of sound-design and disk space...
- Set the midi and audio i/o for the channel from the different drop-down lists. All the options you will find here were created earlier in the device configuration setup stored in your config template. If you would like to change some of it, you can also do it from here with the "midi input setup" and "audio output setup" buttons.
- Press ok.
- The channel is added to the main window and the gig file is loaded into RAM. Well, only the start of the sounds used in the instrument are cached in memory, the main task of LS will be to stream the biggest part of them directly from disk. That's how it's possible to load 30 GBs of samples with only 1 GB of ram.
- You should now be able to play your instrument from jack-keyboard or whatever controller is tied to LS.
If you get no sound, check the volume sliders both on the channel strip and on the main toolbar.
- Repeat these steps as many times as you wish to complete your "sampling orchestra".
- Save your template under a new name so you keep your default template clean if you want to start another orchestra from ground.
Advanced topics
Filtering midi messages before they reach LS
Sometimes sample libraries do not agree with how a composer/arranger expects the sounds played by his MIDI software. A concrete example would be a score editor connected to LS, playing a piano part in the C3 to C4 octave, but what is heard is really one octave higher (C4 to C5). Probably the layering of the samples in the gig file is offset by one octave. If you are sure the mapping is incorrect (opening the gig file in live mode from qsampler can help), then here is some solutions :
- Transpose the MIDI part one octave lower. In an orchestral score, this is very wrong to see notes on staff sounding one octave lower, especially when you already deal with transposing instruments...Also you would have to transpose back before printing.
- Redo the mapping inside the gig file. That would be the best solution as it definitely cures the problem. However this can be a lot of hassle if there is multiple instruments inside the file. Also some non-sounding notes are often reserved before the sounding ones to trigger some cc (keyswitches), making the remapping one octave lower more complex or even impossible.
- The quick and non-destructive way here is to put a MIDI filter between the score editor and LS, that lowers the notes by one octave for the piano channel only. QmidirouteAUR can do that and it also monitors all midi messages along the way. You could for example check that the cc sent by the score are really what they should be (right midi ch, pan, velocity curves etc...)
If you use this setup, you will have to change the piano part MIDI output in your score editor to go to qmidiroute instead of LS, and the piano "channel" in LS to use the qmidiroute output instead of your score editor. This also could be done at the orchestra level if you want to monitor every instrument in your score or if using multiple midi outputs in your score editor is not possible.
If you get the message : Engine: WARNING, CONFIG_EG_MIN_RELEASE_TIME too big for current audio fragment size & sampling rate! and eventually a crash after that, then it's time to reconsider latency for your soundcard.Raise the samples/period setting in qjackctl and retry. As an indication, on an M-audio delta 44, a setup of samples/period=128, periods in buffer=2 and sampling rate=44100 gives a working setup with LS.Latency = 5.8ms which is already quite low.
External Resources
- Homepage
- Article about LS on LinuxJournal
- LS tutorial (french)
- JSampler Manual online
- Links to commercial and free sample libraries
- Rewrite the template configuration wich is too long.
- add status of lv2, dssi plugins version of LS = OK (in overview)
- Write a short section about LS as a plugin, involving different hosts (mostly prerequisite programs and command lines)
- In a quick test, LS lv2 plugin works great.Test host was "elven" from "ll-plugins" package
- addjsampler-fantasia in the install section and configuration section
- jsampler working with openjdk6 or jre.jsampler-cvs slow graphics with openjdk6 (on xf86-video-ati video driver), ok with jre
- add options at build time in advanced topics


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When Mike Finn started Crestwood Builders in 1962, most homes were built by hand by experienced craftsmen.
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Difference between revisions of "Varrios Los Aztecas"
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The '''Varrios Los Aztecas''' (also known as the '''VLA''' or just the '''Aztecas''') is a street gang in [[Grand Theft Auto: San Andreas]]
The '''Varrios Los Aztecas''' (also known as the '''VLA''' or just the '''Aztecas''') is a street gang in [[Grand Theft Auto: San Andreas]]
{{infobox gang
{{infobox gang
Revision as of 14:47, 9 April 2013
The Varrios Los Aztecas (also known as the VLA or just the Aztecas) is a Los Santos based street gang in Grand Theft Auto: San Andreas
Varrios Los Aztecas
Members of the Varrios Los Aztecas
|GTA San Andreas
|El Corona
Little Mexico
Unity Station
|Mexican Street gang
|San Fierro Rifa
Los Santos Vagos
Grove Street Families
|Grove Street Families (briefly)
Carl Johnson
Kendl Johnson
Tec9 (missions only)
Katana (Los Desperados mission only)
RPG (Los Desperados mission only)
|Illegal Street racing
Gun-running/Arms dealing
|Cesar's Home in El Corona
Unity Station
|Cesar Vialpando
Hazer (Possibly Deceased)
The Varrios Los Aztecas are a Mexican gang based Los Santos. Led by Cesar Vialpando, they feature in Grand Theft Auto: San Andreas. They are significantly less prominent than another Mexican gang in the city, their sworn enemies, the Los Santos Vagos. They dislike the San Fierro Rifa, and are also believed to be on bad terms with the Ballas. The Varrios and Grove Street Families are affiliated with each other, due to Cesar's relationship with Kendl Johnson, and his friendship with Carl Johnson, but this does not stop Aztecas and Grove Street members attacking each other on the streets. The Varrios are believed to be based on the Sureños.
The Varrios are traditionally anti-narcotics, with heavy involvement in gun running and street violence, and they only have a few territories compared to other gangs, and these are clustered around the south-western areas of Eastern Los Santos. Varrios Los Aztecas members are mostly seen wearing turquoise bandanas and sunglasses, dressed in 'cholo' style clothing of the time. Sunny, Gal and Hazer are other gang veterans who help Cesar and Carl recover some of their lost territory near the end of the game. The Varrios are also traditionally into low-riding and have betting competitions which are called the Lowrider Challenge which can be found at Unity Station after talking to a man with a bandana and gray working outfit on the outside wall of the station's parking lot. Los Aztecas are seen driving the Broadway, the Hermes and the Glendale.
Their favorite radio station is Playback FM.
The Varrios Los Aztecas are a Mexican street gang that have been described as an "extremely dangerous Hispanic street gang" and as "violent, proud and psychotic". They are heavily involved in arms dealing/gun-running, gang-banging, gang warfare, street violence, murder, illegal street racing, low-riding and vandalism.
- The territories of the Varrios Los Aztecas are 4 and, depending on the in-game days, are available during and after the mission Home Coming (it is been taken over by the Los Santos Vagos during that time, making the total territory counts to 57 instead of 53 originally). And it is unavailable after the mission Los Desperados because the Varrios Los Aztecas is taken over the territory (Going back the total territory counts to 53).
- Strangely, despite Cesar and CJ's alliance, the Varrios Los Aztecas will occasionally attack CJ with no provocation whatsoever. They will always follow him, taunting and insulting the Grove the entire way. Even if the player responds negatively to wearing Grove colors, the Aztecas will still sometimes attack anyway. They are just as hostile as any other enemy gang.


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MISSISSIPPI STATE, Miss. — The cost of fertilizer and strong market prices are inspiring Mississippi growers to increase their soybean acreage in 2004. Robert Martin, Sharkey and Issaquena county director for Mississippi State University's Extension Service, said growers see more potential in soybeans this year than they have in past years.
"A lot of growers are planting early soybeans, hoping to cash in on premium prices in August," Martin said. "Another big factor is that soybeans require less fertilizer than some of the other crops, especially corn. Fertilizer costs are tied closely to the price of fuel, so it's very expensive right now."
John Anderson, Extension agricultural economist, said at the end of March, prices on harvest-time soybean futures were running more than $2.50 per bushel better than last year. November beans were around $7.70 per bushel, compared to just over $5 in 2003.
"From a historical perspective, soybeans are posting excellent prices. When futures prices for next year's crop look this good, more growers will feel encouraged to plant soybeans this spring," Anderson said.
The U.S. Department of Agriculture's prospective plantings report released March 31 forecasts 1.65 million acres of soybeans in Mississippi, an increase of 15 percent. Last year, Mississippi growers harvested a record 39 bushels per acre, surpassing the previous record by 6 bushels.
"Corn prices are also attractive to growers, but fertilizer prices are moving more growers toward soybeans," Anderson said. "December corn futures prices are running near $3.30 per bushel, compared to $2.40 at this time last year."
The USDA report predicts Mississippi growers will decrease their corn acreage to 450,000, down 18 percent. Last year, Mississippi growers harvested a record 135 bushels per acre, surpassing the previous record by 5 bushels.
"Cotton has been able to hold its own in spite of the high soybean prices. Harvest-time cotton futures prices are about 10 percent higher than last year at this time," Anderson said.
The prospective plantings report indicates Mississippi will plant 1.1 million acres of cotton, down just 1 percent. In 2003, growers harvested a record 925 pounds of lint per acre, which was 24 pounds more than the previous record.
Will McCarty, state leader for agriculture and natural resources for MSU's Extension Service, said the decline in cotton acreage simply reflects farmers' reactions to grain prices.
"A rain at the wrong time during planting season could cause that much of a difference. We are seeing more interest in soybeans because of the perception of less risk with higher prices and a lower cost to grow," McCarty said.
Anderson said last year's record yields may help farmers with cash flow issues this spring, but will not have much impact on planting decisions.
"Farmers don't look back as much as they look forward to the price and cost potential," Anderson said.
Mississippi is not alone in its interest in soybeans. The USDA predicts the largest national crop in history, rebounding from three years of decline. Total acres for cotton are also expected to be up 7 percent.
Mississippi's rice acreage is predicted at 235,000, unchanged from 2003. USDA expects the national rice crop to increase 8 percent.
Linda Breazeale writes for MSU Ag Communications.


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Mar 7, 2012 at 1:08 pm
Hey buddy, when are you pulling out of IN for Texarkana? I'll be heading out Friday the 11th.
Jun 1, 2011 at 12:47 am
Happy B-day hope you have a great day!!!!
Jan 21, 2011 at 9:35 pm
Loon! Only a few weeks brother!


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42 U.S. Code § 247b–4g - Repealed.
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Section, Pub. L. 109–450, § 5,Dec. 22, 2006, 120 Stat. 3343, related to establishment and activities of the Interagency Coordinating Council on Prematurity and Low Birthweight.
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