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I've recently been going around trying to find great add-ons to Battlelog and this one really caught my eye. I started out making an account and tried downloading it for my Google Chrome browser, and yet Chrome won't allow me to download it putting me in some despair.
I'm not sure if I should be asking this question on this forum and rather be seeking out learning from the FAQ section. Sorry if I cause any ruckus.
BrainFooLong
Administrator
Quick Answer: Download File, Open Extension Window (Settings -> Extensions), Drop the downloaded CRX File into the extension window.


MYSQL_UPGRADE(1) MySQL Database System MYSQL_UPGRADE(1) NAME mysql_upgrade - check and upgrade MySQL tables SYNOPSIS mysql_upgrade [options] DESCRIPTION mysql_upgrade examines all tables in all databases for incompatibilities with the current version of MySQL Server. mysql_upgrade also upgrades the system tables so that you can take advantage of new privileges or capabilities that might have been added. If mysql_upgrade finds that a table has a possible incompatibility, it performs a table check and, if problems are found, attempts a table repair. If the table cannot be repaired, see Section 2.11.4, “Rebuilding or Repairing Tables or Indexes” for manual table repair strategies. You should execute mysql_upgrade each time you upgrade MySQL. If you install MySQL from RPM packages on Linux, you must install the server and client RPMs. mysql_upgrade is included in the server RPM but requires the client RPM because the latter includes mysqlcheck. (See Section 2.5.1, “Installing MySQL on Linux Using RPM Packages”.) Note On Windows Server 2008, Vista, and newer, you must run mysql_upgrade with administrator privileges. You can do this by running a Command Prompt as Administrator and running the command. Failure to do so may result in the upgrade failing to execute correctly. Caution You should always back up your current MySQL installation before performing an upgrade. See Section 7.2, “Database Backup Methods”. Some upgrade incompatibilities may require special handling before you upgrade your MySQL installation and run mysql_upgrade. See Section 2.11.1, “Upgrading MySQL”, for instructions on determining whether any such incompatibilities apply to your installation and how to handle them. To use mysql_upgrade, make sure that the server is running. Then invoke it like this: shell> mysql_upgrade [options] After running mysql_upgrade, stop the server and restart it so that any changes made to the system tables take effect. If you have multiple MySQL server instances running, invoke mysql_upgrade with connection parameters appropriate for connecting to the desired server. For example, with servers running on the local host on parts 3306 through 3308, upgrade each of them by connecting to the appropriate port: shell> mysql_upgrade --protocol=tcp -P 3306 [other_options] shell> mysql_upgrade --protocol=tcp -P 3307 [other_options] shell> mysql_upgrade --protocol=tcp -P 3308 [other_options] For local host connections on Unix, the --protocol=tcp option forces a connection using TCP/IP rather than the Unix socket file. mysql_upgrade executes the following commands to check and repair tables and to upgrade the system tables: mysqlcheck --no-defaults --all-databases --fix-db-names --fix-table-names mysqlcheck --no-defaults --check-upgrade --all-databases --auto-repair mysql < fix_priv_tables Notes about the preceding commands: · mysql_upgrade also adds --write-binlog or --skip-write-binlog to the mysqlcheck commands, depending on whether the --write-binlog option was specified on the mysql_upgrade command. · Because mysql_upgrade invokes mysqlcheck with the --all-databases option, it processes all tables in all databases, which might take a long time to complete. Each table is locked and therefore unavailable to other sessions while it is being processed. Check and repair operations can be time-consuming, particularly for large tables. · For details about what checks the --check-upgrade option entails, see the description of the FOR UPGRADE option of the CHECK TABLE statement (see Section <IP_ADDRESS>, “CHECK TABLE Syntax”). · fix_priv_tables represents a script generated internally by mysql_upgrade that contains SQL statements to upgrade the tables in the mysql database. All checked and repaired tables are marked with the current MySQL version number. This ensures that next time you run mysql_upgrade with the same version of the server, it can tell whether there is any need to check or repair the table again. mysql_upgrade also saves the MySQL version number in a file named mysql_upgrade_info in the data directory. This is used to quickly check whether all tables have been checked for this release so that table-checking can be skipped. To ignore this file and perform the check regardless, use the --force option. mysql_upgrade does not upgrade the contents of the help tables. For upgrade instructions, see Section 5.1.10, “Server-Side Help”. mysql_upgrade supports the following options, which can be specified on the command line or in the [mysql_upgrade] and [client] groups of an option file. Unrecognized options are passed to mysqlcheck. For information about option files, see Section 4.2.6, “Using Option Files”. · --help Display a short help message and exit. · --basedir=dir_name The path to the MySQL installation directory. This option is accepted for backward compatibility but ignored. It is removed in MySQL 5.7. · --character-sets-dir=path The directory where character sets are installed. See Section 10.5, “Character Set Configuration”. · --compress Compress all information sent between the client and the server if both support compression. · --datadir=dir_name The path to the data directory. This option is accepted for backward compatibility but ignored. It is removed in MySQL 5.7. · --debug[=debug_options], -# [debug_options] Write a debugging log. A typical debug_options string is d:t:o,file_name. The default is d:t:O,/tmp/mysql_upgrade.trace. · --debug-check Print some debugging information when the program exits. · --debug-info, -T Print debugging information and memory and CPU usage statistics when the program exits. · --default-auth=plugin A hint about the client-side authentication plugin to use. See Section 6.3.6, “Pluggable Authentication”. This option was added in MySQL 5.5.10. · --default-character-set=charset_name Use charset_name as the default character set. See Section 10.5, “Character Set Configuration”. · --defaults-extra-file=file_name Read this option file after the global option file but (on Unix) before the user option file. If the file does not exist or is otherwise inaccessible, an error occurs. Before MySQL 5.5.8, file_name must be the full path name to the file. As of MySQL 5.5.8, the name is interpreted relative to the current directory if given as a relative path name. · --defaults-file=file_name Use only the given option file. If the file does not exist or is otherwise inaccessible, an error occurs. Before MySQL 5.5.8, file_name must be the full path name to the file. As of MySQL 5.5.8, the name is interpreted relative to the current directory if given as a relative path name. · --defaults-group-suffix=str Read not only the usual option groups, but also groups with the usual names and a suffix of str. For example, mysql_upgrade normally reads the [client] and [mysql_upgrade] groups. If the --defaults-group-suffix=_other option is given, mysql_upgrade also reads the [client_other] and [mysql_upgrade_other] groups. · --force Ignore the mysql_upgrade_info file and force execution even if mysql_upgrade has already been executed for the current version of MySQL. · --host=host_name, -h host_name Connect to the MySQL server on the given host. · --no-defaults Do not read any option files. If program startup fails due to reading unknown options from an option file, --no-defaults can be used to prevent them from being read. · --password[=password], -p[password] The password to use when connecting to the server. If you use the short option form (-p), you cannot have a space between the option and the password. If you omit the password value following the --password or -p option on the command line, mysql_upgrade prompts for one. Specifying a password on the command line should be considered insecure. See Section <IP_ADDRESS>, “End-User Guidelines for Password Security”. You can use an option file to avoid giving the password on the command line. · --pipe, -W On Windows, connect to the server using a named pipe. This option applies only if the server supports named-pipe connections. · --plugin-dir=path The directory in which to look for plugins. It may be necessary to specify this option if the --default-auth option is used to specify an authentication plugin but mysql_upgrade does not find it. See Section 6.3.6, “Pluggable Authentication”. This option was added in MySQL 5.5.10. · --port=port_num, -P port_num The TCP/IP port number to use for the connection. · --print-defaults Print the program name and all options that it gets from option files. · --protocol={TCP|SOCKET|PIPE|MEMORY} The connection protocol to use for connecting to the server. It is useful when the other connection parameters normally would cause a protocol to be used other than the one you want. For details on the permissible values, see Section 4.2.2, “Connecting to the MySQL Server”. · --shared-memory-base-name=name On Windows, the shared-memory name to use, for connections made using shared memory to a local server. The default value is MYSQL. The shared-memory name is case sensitive. The server must be started with the --shared-memory option to enable shared-memory connections. · --socket=path, -S path For connections to localhost, the Unix socket file to use, or, on Windows, the name of the named pipe to use. · --ssl* Options that begin with --ssl specify whether to connect to the server using SSL and indicate where to find SSL keys and certificates. See Section <IP_ADDRESS>, “SSL Command Options”. · --tmpdir=dir_name, -t path The path name of the directory to use for creating temporary files. · --upgrade-system-tables, -s Upgrade only the system tables, do not upgrade data. · --user=user_name, -u user_name The MySQL user name to use when connecting to the server. The default user name is root. · --verbose Verbose mode. Print more information about what the program does. · --version-check, -k Check the version of the server to which mysql_upgrade is connecting to verify that it is the same as the version for which mysql_upgrade was built. If not, mysql_upgrade exits. This option is enabled by default; to disable the check, use --skip-version-check. This option was added in MySQL 5.5.32. · --write-binlog Cause binary logging to be enabled while mysql_upgrade runs. This is the default behavior; to disable binary logging during the upgrade, use the inverse of this option (that is, start the program with --skip-write-binlog). COPYRIGHT Copyright © 1997, 2015, Oracle and/or its affiliates. All rights reserved. This documentation is free software; you can redistribute it and/or modify it only under the terms of the GNU General Public License as published by the Free Software Foundation; version 2 of the License. This documentation is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with the program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA or see http://www.gnu.org/licenses/. SEE ALSO For more information, please refer to the MySQL Reference Manual, which may already be installed locally and which is also available online at http://dev.mysql.com/doc/. AUTHOR Oracle Corporation (http://dev.mysql.com/). MySQL 5.5 02/26/2015 MYSQL_UPGRADE(1)


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I had the great pleasure of participating in the first Hawaii Annual Code Challenge, held from August 27-September 24, 2016. The goal of HACC is to “engage the local tech community in the modernization of Hawaii State Government” through a month-long hackathon to develop solutions to a pre-selected set of problems faced by community organizations. Here were the choices for 2016:
| Organization | Problem |
|---|---|
| Oahu Community Correctional Facility | A more efficient way to schedule over 300 visits per week by over 8000 approved visitors |
| Hawaii Farmer's Markets | A centralized portal providing information regarding 200+ markets statewide; |
| Hawaii Agriculture Food Products | Increased visibility and access to locally grown products |
| Department of Health | Help people with disabilities to compete more effectively for jobs. |
| IHS | Help homelessness outreach teams respond more effectively to community referrals. |
| Department of Community Services | Provide a yelp-like application that enables the elderly and their care providers to find services. |
I’ve been involved with many hackathons, but several things about HACC make it stand out:
A focus on helping pre-selected community organizations. Many hackathons adopt one of the following two organizing principles: (1) create an app to illustrate a viable business model; or (2) create an app to exercise a technology recently developed by the sponsor of the hackathon. While both of these approaches can be fun, it is refreshing to have a hackathon focus on specific, important community problems and ask the technology community to addresss them as best they can, regardless of whether the solution would appeal to a venture capitalist or utilize some new tech hack.
A month, not a weekend. Many hackathons are 24 to 48 hours long. Such a short duration limits how ambitious a team can be. A month provides more time for research into problem areas, stakeholder engagement, and application refinement.
It’s about Hawaii, not Silicon Valley. Many hackathons have an implicit focus on what would sell in Silicon Valley. HACC is all about Hawaii. I love that.
I went to the HACC kickoff event just to see what HACC was all about. Within a few days I found myself on a team with McKay Davis, Cam Moore, Kelemete Seto, and Mike Peacock. We took on the challenge of creating a scheduling solution for OCCC and implemented a system called Kipa using Meteor and Semantic UI.
Here is a one minute video illustrating the essential features of Kipa:
I am pretty happy with Kipa:
First, we put a lot of design effort into usability. We invested significant time during the month to learn about the OCCC visitation process. One important insight: visitors are usually not technically sophisticated, and may only be able to access a computer at a library. However, a survey we conducted of actual OCCC visitors revealed that most have cell phones with text messaging and would like to use that to communicate about scheduling. Kipa recognizes these constraints and uses SMS whenever possible for communication.
Second, as with virtually any scheduling scenario, there are organization-specific scheduling “gotchas”. As one example, we learned that the 10:00am and 10:30am slots are reserved for female detainees. To enable Kipa to adapt to current and future scheduling peculiarities, we implemented an extensible set of “hooks” to support scheduling constraints.
Third, the application exploits the reactive nature of Meteor, and works well across platforms (desktop, tablet, mobile).
For details on Kipa, including a walkthrough of the system, screen shots, and access to the code, please see the Kipa Home Page.
See the DevPost HACC Submissions Page for links to all the project submissions for HACC 2016.
I am already looking forward to HACC 2017, and encourage every ICS student to participate. Here are some thoughts that I hope will make your experience better.
1. HACC is a super efficient way to build your professional portfolio. Why do HACC? Because in just one month, HACC can provide you with a new, significant project for your portfolio (see mine) showing how you worked in a team to build an interesting solution to an important societal problem. You don’t have to participate in HACC purely out of altruism for Hawaii; you can also do it out of self-interest. Participation in HACC will improve your marketability and maybe even help you land a higher paying job after you graduate.
2. Pick one project and commit to it. Some people participated in two or three HACC teams simultaneously in 2016. After seeing the results, I don’t recommend it, because during the “crunch time” (i.e. the last week) you’ll have to split your time between multiple projects just when each project (and team) is hoping for your undivided attention. I think it’s better to put all your eggs in one basket and create the best possible single submission.
3. If at all possible, build a team that includes a videographer. Now that you’ve watched my little screencast about Kipa above, compare it to this video from the winning team:
Wow. There’s just no doubt about it: this video is stunning and head-and-shoulders above every other team’s video submission. The video is not just technically impressive; it tells a story about the project. The actual Ohai application only implements a few static HTML page mockups, but the team did a superb job of communicating stakeholder requirements.
Finding someone with video experience can be tricky, but the UH Academy for Creative Media, Department of Communications, and even the Lava Lab can be source of students with this skill set.
4. A mobile CRUD app is the baseline. Most of the competitive submissions implemented a CRUD application that could be displayed on a smart phone. Any student who has taken ICS 314 will have more than enough background to satisfy this baseline criteria for success. If you haven’t taken 314, find someone for your team who has!
5. Augment your mobile CRUD app with some special sauce. A month provides you with enough time to develop your app beyond CRUD. For example, Kipa extends a mobile CRUD app for OCCC scheduling with three special sauces: (1) reactivity, (2) text messaging for communication, and (3) an extensible constraint system.
Fortunately, the ICS degree program provides a wealth of material for you to apply to your HACC project, including: security, recommendation engines, advanced visualizations, concurrent programming, machine learning, robotics, game mechanics, medical informatics, etc. You might even consider using Raspberry PI or Arduino boards to craft an Internet of Things solution.
6. Try to have users. A month is plenty of time to build an initial version of your application and obtain user feedback. Depending up the organization and application topic, you could release your initial version after two weeks, and grow a community of 10, 100, or 1000 users by the end of the four week hackathon period.
7. Get ICS credits for HACC 2017. I plan to offer a 3 credit ICS 499 Independent Study course in Fall, 2017 for students who wish to: (1) participate in the Hackathon during August and September, then (2) continue development of the application for the remainder of the semester. Contact me if you’re interested.
8. Build it for Hawaii and for your portfolio, not for the judges. It’s hard to be a judge for HACC: they have very little time to evaluate the submissions, and (at least in 2016) there were a lot of final submissions to evaluate. I learned from veteran hackathon participants about “strategies” to make the submission more superficially appealing to judges. My advice: don’t play the “game”; just build the best possible system that you can in the time you’ve been given.


library(tidyverse)
library(cowplot)
library(broom)
library(modelr)
library(viridis)
library(lubridate)
library(hms)
library(knitr)
library(kableExtra)
knitr::opts_chunk$set(tidy.opts=list(width.cutoff=60),tidy=TRUE, echo = TRUE, message=FALSE, warning=FALSE, fig.align="center")
source("../../IDA/tools/plotting_tools.R")
theme_set(theme_1())
On 06/10/19 I tried a first attempt with PYO in 1% agarose +/- 50% glycerol, to try perturbing the effective diffusion coefficient measured by FRAP. This failed, and I saw photoactivation instead of any type of FRAP. I thought of a number of reasons why this might be and possible solutions, so I tried again with more concentration so glycerol. I reasoned that even if the photoactivation was real that it may not be a problem at lower concentrations. The other explanation I considered was that perhaps the TCEP did not diffuse/react as quickly in the glycerol gel, and maybe it just needed longer to reduce the PYO.
For this experiment I setup 1% agarose gels with 0, 10, 20, and 50% glycerol with PYO in the same format as last time. I also tried two gels with PCA instead of PYO, but I was not able to FRAP PCA at all.
It is a reasonable expectation that glycerol makes the solvent more viscous and slows diffusion. Here’s one reference that suggests we should see a decrease of 2-5x over this range of glycerol.
I made the agarose pads very similarly to how I did on 06/10. I made up the appropriate PBS - glycerol mixtures (1x PBS final concentration) using 2x and 1x PBS and pure glycerol. Then I dissolved the agarose in the solutions (~20mL) and microwaved to dissolve. The molten gels were stored in the 60 degree water bath, while I aliquoted the appropriate amount of PYO (300uM final) or PCA (500uM final) into fresh 15mL tubes. Then I mixed 3mL of the appropriate agarose - glycerol, vortexed and then let the tubes briefly settle in the water bath before pouring into the coverslip bottom mattek dishes.
The gels were left to solidify at room temp for a full hour, since I knew that the glycerol gels take longer to solidify. Then I added 90uL of TCEP stock to each dish before I even left the lab, which gave it plenty of time to incubate. Here’s a picture about 1.5 hrs after adding the TCEP. You can see obvious PYO reduction in all three of the glycerol gels shown (the 0% glycerol pad was on the microscope), and you can see the greenish color of reduced PCA in the 0% glycerol PCA gel. So, either waiting longer for the gel to solidify or for the TCEP reduce facilitated PYO reduction even in the 50% glycerol gel as compared to the weirdness on 06/10.
knitr::include_graphics("Photos/IMG_20190613_144416.jpg")
Other photos of the gels are in the Photos directory in this directory.
I did not take a picture of the settings this time, but they were very similar to 06/10. See the file names for some descriptions of the parameters. All images were collected in 16bit. The only notable change I made for some of the PYO FRAP acquisitions is that I first acquired at a 50ms frame rate (128px frame) as before (called “rep”). Subsequently I was able to acquire at a framerate of 12ms (I think?), by checking the “acquisition” check box for the bleached circle in the “regions” menu. This told the microscope to only image the 50um radius bleached circle and not the other pixels in the image. Fewer pixels to acquire enabled faster framerate, but we could not estimate the effective bleach radius or the background signal. However, because I just acquired bleaches with the whole frame I think it would be safe to extrapolate from those slower “rep” acquisitions.
Also important to consider, I tried bleaching at 350nm with the two photon and at 405nm with the diode and neither worked better than 375. This means that we are bleaching and acquiring using the two photon laser, which has a very thin cross section - pinhole ~ 4um. Therefore, by bleaching a disc 100um wide and 4um thick, most of the fluorescence recovery will be coming from the top and bottom of the disc, not the edges (x-y). Therefore I think I need to think harder about how to estimate the vertical “nominal” and “effective” bleach radii in order to quantify accurately.
I did try FRAP on the PCA gel (0% glycerol), but there was absolutely no detectable bleaching using the 405 or two photon lasers (350 - 400nm) or both. That data along with the initial tests etc is all in the google sheet. The dataset in this notebook is specifically for the PYO pads at different concentrations of glycerol.
Let’s read in the dataset.
df <- read_csv("06_13_19_PYO_FRAP_glycerols_data.csv")
df
## # A tibble: 10,850 x 14
## img_num time bleach_int ref_int filename condition agarose PYO
## <dbl> <dbl> <dbl> <dbl> <chr> <chr> <chr> <chr>
## 1 1 0 3283. 3299. 0pctGly… 0pctGlyc 1pctAg 300u…
## 2 2 0.172 3172. 3221. 0pctGly… 0pctGlyc 1pctAg 300u…
## 3 3 0.524 3234. 3134. 0pctGly… 0pctGlyc 1pctAg 300u…
## 4 4 0.712 3160. 3154. 0pctGly… 0pctGlyc 1pctAg 300u…
## 5 5 0.895 3153. 3213. 0pctGly… 0pctGlyc 1pctAg 300u…
## 6 6 1.08 3205. 3093. 0pctGly… 0pctGlyc 1pctAg 300u…
## 7 7 1.26 3141. 3284. 0pctGly… 0pctGlyc 1pctAg 300u…
## 8 8 1.44 3142. 3150. 0pctGly… 0pctGlyc 1pctAg 300u…
## 9 9 1.61 2960. 3193. 0pctGly… 0pctGlyc 1pctAg 300u…
## 10 10 1.79 3157. 3066. 0pctGly… 0pctGlyc 1pctAg 300u…
## # … with 10,840 more rows, and 6 more variables: objective <chr>,
## # frames <chr>, excitation <chr>, bleach <chr>, fast <chr>, id <dbl>
Plotting the data looks like this for the 50ms framerate acquisitions (called “rep”):
ggplot(df %>% filter(fast == "rep"), aes(x = time, y = bleach_int,
group = id)) + geom_path(alpha = 0.25) + facet_wrap(fast ~
condition, scales = "free")
And here’s what the 12ms acquisitions look like (called ‘repFAST’):
ggplot(df %>% filter(fast == "repFAST"), aes(x = time, y = bleach_int,
group = id)) + geom_path(alpha = 0.25) + facet_wrap(fast ~
condition, scales = "free")
Already we can see that maybe the recovery isn’t as sharp in the 50% glycerol condition. It’s hard to tell with the others. Also note that the replicates all seem to overlap pretty well. It’s hard to tell whether the faster framerate helped or not, but we’ll come back to that. You can also see that we are consistently getting a 10 - 20% bleach, which is great compared to where we started!
Ok to quantify the data we need to singly normalize the data by the initial fluorescence.
df_baselines <- df %>% group_by(condition, fast, id) %>% filter(img_num <=
10) %>% summarise(avg_baseline = mean(bleach_int))
df_single_norm <- left_join(df, df_baselines, by = c("condition",
"fast", "id")) %>% mutate(single_norm_int = bleach_int/avg_baseline)
ggplot(df_single_norm, aes(x = time, y = single_norm_int, group = id)) +
geom_path(alpha = 0.25) + facet_grid(fast ~ condition, scales = "free")
Next we will do the full scale normalization to account for the amount that was bleached.
df_full_norm <- df_single_norm %>% group_by(condition, fast,
id) %>% mutate(min_single_norm_int = min(single_norm_int)) %>%
mutate(full_norm_int = (single_norm_int - min_single_norm_int)/(1 -
min_single_norm_int))
ggplot(df_full_norm, aes(x = time, y = full_norm_int, group = id)) +
geom_path(alpha = 0.25) + facet_grid(fast ~ condition, scales = "free")
Then we need to normalize the bleach to t = 0.
df_full_fit <- df_full_norm %>% filter(time > 5) %>% group_by(condition,
fast, id) %>% mutate(min_time = min(time)) %>% mutate(norm_time = time -
min_time)
ggplot(df_full_fit, aes(x = norm_time, y = full_norm_int, group = id)) +
geom_line(alpha = 0.25) + facet_grid(fast ~ condition, scales = "free")
Normalization looks good. Let’s directly compare the fast and slow acquisition rates:
ggplot(df_full_fit, aes(x = norm_time, y = full_norm_int, color = fast,
group = id)) + geom_line(alpha = 0.25) + facet_wrap(~condition,
scales = "free")
The shorter time scales repFAST measurements overlay the rep acquisitions very well. It’s still not obvious if the two framerates will make a big difference…
Finally, we can fit the recovery with our single exponential model. Here’s the slow acquisition first:
ggplot(df_full_fit %>% filter(fast == "rep"), aes(x = norm_time,
y = full_norm_int)) + geom_point(shape = 21, alpha = 0.5) +
geom_smooth(method = "nls", formula = y ~ (I0 - a * exp(-B *
x)), method.args = list(start = c(I0 = 0.85, a = 0.5,
B = 0.2)), se = F) + facet_grid(id ~ condition, scales = "free")
The fits seem pretty good overall. Let’s pool all the conditions and see if we can simply see a difference in the fit of the whole dataset.
ggplot(df_full_fit %>% filter(fast == "rep"), aes(x = norm_time,
y = full_norm_int, color = condition)) + geom_point(shape = 21,
alpha = 0.25) + geom_smooth(method = "nls", formula = y ~
(I0 - a * exp(-B * x)), method.args = list(start = c(I0 = 0.85,
a = 0.5, B = 0.2)), se = F) + scale_color_viridis_d()
Wow! We can the expected trend here and a few other things - First, the higher the percentage glycerol the slower the recovery seems to be. This is obvious for the 50pct glycerol, but actually for the 10 and 20% it’s less obvious. 10 and 20 could just look shallower because the recovery is less complete than 0% glycerol. We’ll have to look at the parameter estimations to be sure.
Let’s now look at the same type of plots for the fast framerate data:
ggplot(df_full_fit %>% filter(fast == "repFAST"), aes(x = norm_time,
y = full_norm_int)) + geom_point(shape = 21, alpha = 0.5) +
geom_smooth(method = "nls", formula = y ~ (I0 - a * exp(-B *
x)), method.args = list(start = c(I0 = 0.85, a = 0.5,
B = 0.2)), se = F) + facet_grid(id ~ condition, scales = "free")
Again, the fits look reasonably good. Let’s see what happens when we pool all the replicates:
ggplot(df_full_fit %>% filter(fast == "repFAST"), aes(x = norm_time,
y = full_norm_int, color = condition)) + geom_point(shape = 21,
alpha = 0.25) + geom_smooth(method = "nls", formula = y ~
(I0 - a * exp(-B * x)), method.args = list(start = c(I0 = 0.85,
a = 0.5, B = 0.2)), se = F) + scale_color_viridis_d()
Nice! So we see the same trend as above. The 50% glycerol recovery seems to clearly be slower, and maybe the 20% does too. We also have the same confounding visual that the recovery is less complete when glycerol is added, so let’s move on to some parameter estimation.
As before, we are fitting with a single exponential model of the form:
\[ I_{fit} = I_0 - \alpha e^{- \beta t}\]
Which gives the half recovery time:
\[\tau_{1/2} = \frac{ln(2)}{\beta}\]
Which then gives the diffusion coefficient:
\[D = 0.224 \frac{r^2}{\tau_{1/2}}\]
And corrected for bleaching that is not instantaneous:
\[D = \frac{r_e^2 + r_n^2}{8 \tau_{1/2}}\] Where \(r_e\) is the effective bleach radius (determined from first image post bleach) and \(r_n\) is the nominal bleach radius that was where the laser was setup to scan. This is where the tricky part about the two-photon acquisition comes in - we’ll get back to this at the end.
Ok, so let’s fit the model and extract the coefficients. First the slow acquisition:
sing_exp_coef <- NULL
sing_exp_coef <- df_full_fit %>% group_by(condition, fast, id) %>%
do(tidy(nls(formula = full_norm_int ~ I0 - a * exp(-B * norm_time),
data = ., start = list(I0 = 0.85, a = 0.5, B = 0.2),
control = nls.control(tol = 1e-07)), conf.int = T))
ggplot(sing_exp_coef %>% filter(fast == "rep"), aes(x = condition,
y = estimate, color = condition)) + geom_pointrange(aes(ymin = conf.low,
ymax = conf.high), position = position_jitter(width = 0.1)) +
facet_wrap(~term, scales = "free", ncol = 1) + scale_color_viridis_d()
And the fast acquisition:
ggplot(sing_exp_coef %>% filter(fast == "repFAST"), aes(x = condition,
y = estimate, color = condition)) + geom_pointrange(aes(ymin = conf.low,
ymax = conf.high), position = position_jitter(width = 0.1)) +
facet_wrap(~term, scales = "free", ncol = 1) + scale_color_viridis_d()
Ok, so we can see the same trends in the two types of acquisitions. \(a\) and \(I_0\) and \(\beta\) all decrease with increasing glycerol. Remember that \(\beta\) is what determines the half recovery time and therefore the diffusion coefficient, so let’s focus on that. Although there are 2 fewer replicates for the fast acquisition times, it seems clearer in the fast data that \(\beta\) is decreasing with added glycerol. The error bars seem tighter for the fast acquisition set. Let’s go ahead and calculate the \(\tau_{1/2}\) for the datasets:
tau_est <- sing_exp_coef %>% filter(term == "B") %>% mutate(tau_mean = log(2)/estimate) %>%
mutate(tau_low = log(2)/conf.low) %>% mutate(tau_high = log(2)/conf.high)
ggplot(tau_est, aes(x = condition, y = tau_mean, color = condition)) +
geom_pointrange(aes(ymin = tau_low, ymax = tau_high), position = position_jitter(width = 0.1)) +
scale_color_viridis_d() + facet_wrap(~fast, scales = "free",
ncol = 1) + ylim(0, 10)
So as expected the changes in \(\beta\) show up as increasing half recovery times. There seems to be a difference separating 0 from 50% glycerol of ~4-5 seconds. Now’s a good time to refer back to the FRAP curves. Let’s look at a few examples:
ggplot(df_full_fit %>% filter(fast == "repFAST"), aes(x = norm_time,
y = full_norm_int, color = condition)) + geom_hline(yintercept = 0.5,
linetype = "dashed") + geom_point(shape = 21, alpha = 0.5) +
scale_color_viridis_d() + xlim(0, 20) + facet_wrap(~condition,
scales = "free") + ylim(0, 1)
Ok, so these \(\tau_{1/2}\) estimates seem to make sense. I plotted a line at 0.5 normalized intensity here, remember that half recovery is actually half of the recovery, \(I_0\), not all the way to 1, so there is some bias in the above plot. Really all the dotted lines should vary from 0.425 (half highest 0% I0) to 0.33 (half lowest 50% I0), but I think it still makes sense and visually there is a difference.
Now let’s calculate our \(D_{eff}\) using just the nominal bleach radius of 50um (ignoring the two-photon issue):
r = 0.005
d_est <- tau_est %>% mutate(d_mean = (0.224 * r^2)/tau_mean) %>%
mutate(d_low = (0.224 * r^2)/tau_low) %>% mutate(d_high = (0.224 *
r^2)/tau_high)
ggplot(d_est, aes(x = condition, y = d_mean, color = condition)) +
geom_pointrange(aes(ymin = d_low, ymax = d_high), position = position_jitter(width = 0.1)) +
scale_color_viridis_d() + facet_wrap(~fast, scales = "free",
ncol = 1) + ylim(5e-07, 2.5e-06)
And the effective radius corrected version:
r_n = 0.005
r_e = 0.01
d_mod_est <- tau_est %>% mutate(d_mean = ((r_n^2) + (r_e^2))/(8 *
tau_mean)) %>% mutate(d_low = ((r_n^2) + (r_e^2))/(8 * tau_low)) %>%
mutate(d_high = ((r_n^2) + (r_e^2))/(8 * tau_high))
ggplot(d_mod_est, aes(x = condition, y = d_mean, color = condition)) +
geom_pointrange(aes(ymin = d_low, ymax = d_high), position = position_jitter(width = 0.1)) +
scale_color_viridis_d() + facet_wrap(~fast, scales = "free",
ncol = 1) + ylim(1.5e-06, 6.5e-06)
Let’s see what happens to this estimate if we assume that instead of the x-y radius, that the relevant parameter is the z radius produced by the thin plane excited by the 2p laser. The pinhole was ~4.4um, so let’s consider that the nominal diameter, so the nominal radius is \(r_n = 2.2 \mu m\). Let’s assume for the moment that the effective bleach radius in Z is the same as in x-y \(r_e = 100 \mu m\). I’m not sure this is a good assumption…but let’s just see:
r_n = 0.00022
r_e = 0.01
d_mod_est <- tau_est %>% mutate(d_mean = ((r_n^2) + (r_e^2))/(8 *
tau_mean)) %>% mutate(d_low = ((r_n^2) + (r_e^2))/(8 * tau_low)) %>%
mutate(d_high = ((r_n^2) + (r_e^2))/(8 * tau_high))
ggplot(d_mod_est, aes(x = condition, y = d_mean, color = condition)) +
geom_pointrange(aes(ymin = d_low, ymax = d_high), position = position_jitter(width = 0.1)) +
scale_color_viridis_d() + facet_wrap(~fast, scales = "free",
ncol = 1)
Ok, so the estimated diffusion coefficient has decreased a little, but it’s still reasonably in the 10^-6 cm^2 / sec range. I think We will need to think about this more seriously.


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C++ is almost a super set of C. If you write any C source code or C source file. C++ compiler will acts as C compiler. This helps in smooth migration of existing C to C++.
A C++ reference is identical to C pointers. But they are safer as they can't be null and can't be uninitialized.
Classes are similar to structs. A member function is a function which take pointer to object of class as an implicit parameter. Class with member function is similar to C struct and a function which takes structs as argument.
class A {
public:
int GetX();
private:
int x;
}
int A::GetX()
{
return x;
}
struct A {
int x;
}
int GetX(struct A * this)
{
return this->x;
}
These are member function that is guaranteed to get called when objects are created and destroyed. This make sure all objects are properly initialized and destroyed. This avoids resource leaks and initilization bugs. There is no way in C to make this implicitly.
C++ namespace allow name reuse in different contexts. This avoids lengthy names with module/context prefixes like C.
A C++ compiler replaces a function call when encounters an overloaded operator. Operator overloading improves the code readability if used properly.
| Vendor | C++ Standard |
|---|---|
| Keil | C++11 |
| ARM | C++14 |
| IAR | C++14 |
| GCC | C++17 |
Please make sure not to connect both external 5 volts power supply and USB power supply at same time.
Download usb driver from https://my.st.com/content/my_st_com/en/products/development-tools/software-development-tools/stm32-software-development-tools/stm32-utilities/stsw-link009.license=1564137466456.product=STSW-LINK009.version=2.0.1.html Run stlinkwinusbinstall batch file to install driver.
Download st link utility from https://my.st.com/content/my_st_com/en/products/development-tools/software-development-tools/stm32-software-development-tools/stm32-programmers/stsw-link004.html
http://openocd.org/doc/html/index.html
OpenOCD is a Open On-Chip debugger that provides programming,debugging boudry-scan testing for embedded device. It acts as a server and acceptss incoming connection from GDB via port 3333 or telnet port 4444.
ST has provided and eclipse based IDE which uses ARM Gcc backend to cross compile firmware. We will use this IDE to write , debug our firmware source code.
arm-none-eabi-g++ --version
Due to limited resources available on target hardware for running build tools development is mostly done on workstation or PC with higher memory and speed. This machine is called host machine and it runs the build tool but generate binary which will run on different (mostly microcontroller) hardware. This process of generating code for different target is called cross compilation.
Compiler translate source code into machine code for individual source file. Output of compilation process is object code.
Linker compose multiple objects file into one single executable file. For gcc toolchain output is mostly ELF. Executable Linker Format ELF file contains different sections
This section contains executable instructions of program. Controller's program counter always access instructions from this memory area.
Contains read only values like constants. This section can be mapped to read only memory area.
Containing the values of all the initialized variables of the program, accessible in the read/write mode at runtime. It is a section that contains all the variables, static or global, that have been initialized in the code. This area is remap to writable memory area as these values will be changing during program life time.
This section reserved all uninitialized variables and objects accessible during program runtime for modification. Because there in no values here ELF only describes this section but do not provide any contents. Startup code should initialize bss section to zero.
Every embedded target has different memory layout for program and data memory. Hence during linking process a custom linker script describing memory layout of target should be provided.
ELF file will be loaded to target system using programming tools or debug probes. ELF files need to be converted to format like intel hex or bin which then can be loaded at non volatile memory location accessible by program counter.
Upon reset controller will start executing text section loaded at reset address.
The linker script is a file containing the description of the memory sections in the target, which need to be known in advance in order for the linker to place the symbols in the correct sections in flash, and instruct the firmware components about special locations in the memory mapping area that can be referenced in the code.
The file is recognizable by its .ld extension, and it is written in a specific language. As a rule of thumb, all the symbols from every single compiled object are grouped in the sections of the final executable image.
Beside standard sections we can instruct linker to reserve custom sectors.
For eg. To calculate CRC of flash image we need to make sure unused sectors are filled with known values.
const uint8_t
__attribute__((section(“.crcfill”)))
private_key[100] = {0};
Literals are tokens of C++ program that represent constant values embedded in source code.
| Literal |
Linker file
ELf file consists of additional header information but to load binary on target flash we need to strip down this additional information.
arm-none-eabi-objcopy -I elf -O binary firmware.elf firmware.bin
st-link_cli -C SWD -P firmware.bin 0x8000000 -V "after_programming"
#+SRCBEGIN C++ namespece stm32f767::Uart { classes Uart1 { } } #+SRCEND
Staring from C++ 11 we can now initialize class member variables in class declaration.
#+BEGINSRC class SerialSettings { private: uint32t mbaudrate = 9600; } #+ENDSRC_
inline
keyword requeset compiler to replace code call with actual code contents to avoid overhead of function call.
This will help in catching logical errors early in compile time. Basic sytax is
static_assert ( bool_constexpr , message )
An enumeration is a distinct type whose values are restricted to a range of values. Intenally enumerations are of integer type. But C++ enumeration are more strongly typed compared to C. In C enum and interger are interchangeble but in C++ not unless explicitly casted.
Starting from C++ 11 we can now tell compiler to allocate specific size of enumerations constans.
This helps in situations where we need fix size of enumerations like protocols parser, we can directly use enumerations values in transmit or recieve buffer.
#include <stdio.h>
enum command { ON, OFF};
enum command c;
int main ()
{
printf ("Hello World %d",sizeof(c));
return 0;
}
#include <iostream>
enum class command : char { ON, OFF};
enum class functioncode : short { READ, WRTE, UPDATE };
int main ()
{
std::cout << "scoped enum with size for command = "
<< sizeof(command) << std::endl ;
std::cout << "scoped enum with size for functioncode = "
<< sizeof(functioncode) << std::endl ;
return 0;
}
For specific device classes we don't want to create duplicate copy of same peripheral object. We can make sure nobody can accidently copy object we will delete copy constructor.
typedef bool (*Transmit)(char *); using Transmit = bool(*)(char *);
return_type operator operator_symbol (list of parameters)
We will write hello world program which will print "Hello World of C++ " sting to serial port using micro controller UART3.
C++ compiler will use name mangeling hence functions name used by user will have diffrent name for compiler. Hence if you want to use a function from C library we should tell compiler not to change its name by telling compiler for C linkage.
extern int C_library_function(void);
To do this on entire header file with exported functions we can used
extern int C_library_function(void);
https://hackaday.com/2015/11/13/code-craft-embedding-c-timing-virtual-functions/
https://gcc.gnu.org/onlinedocs/cpp/Common-Predefined-Macros.html
http://www.keil.com/support/man/docs/armlib/armlib_chr1358938908603.htm
C++ libraries need C libraries for target specific support.
Introduce students to basic C++ development process by showing Hello world string on serial port using virtual com port of nucleo platform.
Constructor overloading to use non default baud rate settings.
We will now start exploring object oriented programmin paradigms.
Till now for every uart change we have to create individual objects of individual classe. Using inheritance feature we will create a base class interface for uart which then be overridden by individual subclasses. https://github.com/prasadghole/embeddedCppTrainingProjects/releases/tag/Serial_1
Implement class for Uart Port 3
https://github.com/prasadghole/embeddedCppTrainingProjects/tree/master/SerialPort_Interface_AllUart
Mostly this can be exercise for students. Instead of createing pin wise subclasses we can create port wise classes.
Create a wrapper class (adapter pattern) so that for every board type we don't need to pass pin every time we call api.
How to integrate interrupt handlers. We will show case using member function.
ISR handlers can be made using static functions.
GPIO class is interface is mixture of pin vs port functons. Need to refactor so that pin and functons are binded togethor.


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{{ date }}
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Dear {{ first_name }},
I am pleased to offer you an appointment as a Teaching Assistant in Some Department. The starting date of your appointment will be {{ start_date | date: "%b %d, %Y" }} and this appointment will end on {{ end_date | date: "%b %d, %Y" }} with no further notice to you.
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In the event that you have a disability that would impact upon
how you would respond to an emergency in the workplace (e.g.,
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Your duties may include all or any combination of the following: grading, scheduled tutorials, office hours, Math Aid Centre hours, and test and exam invigilation. You will be expected to complete all grading for all student work that is completed during the term of the appointment, up to and including final exams.
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If you have any questions, please contact me via email at {{ ta_coordinator_email }}
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--- layout: post title: Knitting Stash, an Android App tags: android knitting java category: Underhill Labs --- Knitting Stash is a knitting app for android devices. It is a suite of tools that helps you keep track of your knitting needles, crochet hooks, projects and all of your counters.


THE BOYS
Australia, 1997
Rated MA in Australia
Cast: David Wenham, Toni Collette, Lynette Curran, John Polson, Anthony Hayes.
Director: Rowan Woods
Producers: Robert Connolly, Douglas Cummins, John Maynard, David Wenham
Writers: Gordon Graham (play), Stephen Sewell
This is a disturbing and riveting movie. It opens with Brett Sprague (Wenham) being released from jail and is picked up by one of his brothers, Stevie (Hayes). It's not long before we find out that Brett is the alpha-male of this little pack.
Almost immediately we leap forward in time 18 hours. Hints abound that something bad, very bad, has happened. Police radios crackle. Brett and his two brothers have been arrested. A brief glimpse of something unspeakable.
Then, just as quickly, we fade back to the 'present' as Brett arrives home to the domestic non-bliss of his mother's house. The characters are introduced: Brett's other brother Glenn (Polson), Brett's girlfriend, Michelle (Collette). His mum Sandra (Curren, the wonderful Betty in "Bliss"). Stevie's little girl lost (and pregnant and unloved) 'girlfriend' Nola. Tensions are building up inside the house. Brett seems to have a tranquil venom about him - calm on the surface, but the snake is in their.
What is disturbing is that we - as viewers - know from almost the opening credits that something terrible is going to happen. We are shown the aftermath in assorted flash-forwards: Brett burning clothes in the back yard, Brett and brothers in jail etc.
These hints are interleaved with the story of the day of Brett's return home. We see a family in trouble.  Nola talks about escaping this slow motion prison. Michelle taunts Brett. Brett taunts and accuses everybody. And poor Mum tries to hold it all together by cooking up a nice Welcome Home dinner.
The intensity builds up as we flip back between the 'now' and even further forward in time (sentencing, trial). But the audience is never told - during these future bites - who the victim was or even what the crime was. Is it the poor, sweet mother? The moping Nola? The defiant Michelle? The man who put Brett in jail in the first place? The 'now' story leaves enough threads open so that it could be any of them. It is inevitable, this evil. And there is nothing we can do but sit there in the dark cinema and wait for it.
Wenham is outstanding in the lead role. His Brett has a quiet, brewing evilness such that he dominates nearly every scene he is in. Most of the film takes place inside the house, indeed the film is based upon a play. There is virtually no music on the soundtrack.
The performance of David Wenham alone makes this film worth seeing. Add in very good supporting roles, direction, editing, production and script…and the mix is distressing and challenging. At a running time of a crisp 82 minutes, your time won't be wasted. 4.5 out of 5.
(The film seems to have had a 2nd wind here. Wenham is enjoying the lead role in a hugely successful TV series "Sea Change", which started on TV after "The Boys" had been released. I first saw "The Boys" about 2 months ago. I saw it again today and there were a lot more people in the audience this time around. In " Sea Change" Wenham shows his versatility by playing very much an anti-Brett role: the romantic lead - a gentle, kind, good bloke. Hopefully both will hit your shores soon)
Copyright © David Sidwell 1998
-- review end ---
David Sidwell (Williamstown, Australia )
<EMAIL_ADDRESS>or<EMAIL_ADDRESS>http://connexus.apana.org.au/~dsidwell
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Voice sampling is a very interesting topic as it tells how the voice data (analog) is converted to digital data.
Terms Used:
When converting an voice (analog) signal , there are two things to focus: sampling and quantization. Together, they determine the quality of the digitized sound.
Sampling
: is about the sampling rate — i.e. how many samples per second you use to encode the sound. The sampling rate must be double the highest frequency in the signal so that signal neither appears choppy not too smooth.Quantization
: is about how many bits you use to represent each sample. The number of bits determines the number of different values you can represent with each sample.Nyquist Theorem
Digital signal technology is based on the premise stated in the Nyquist Theorem: when a signal is instantaneously sampled at the transmitter in regular intervals and has a rate of at least twice the highest channel frequency, then the samples will contain sufficient information to allow an accurate reconstruction of the signal at the receiver
PC: Cisco
Example: Nyquist Theorem
While the human ear can sense sounds from 20 to 20,000 Hz, and speech encompasses sounds from about 200 to 9000 Hz,the telephone channel was designed to operate at about 300 to 3400 Hz. This economical range carries enough fidelity to allow callers to identify the party at the far end and sense their mood.
Nyquist decided to extend the digitization to 4000 Hz, to capture higher-frequency sounds that the telephone channel may deliver.
Therefore, the highest frequency for voice is 4000 Hz, or 8000 samples per second; that is, one sample every 125 microseconds.
Several people have experienced that voice over phone is not exactly similar to their own voice. If we increase sampling rate and number of bits for quantization( that means also increasing number of levels), then the similarity in the voice will improve.
In other words we can say that we will send more information over the voice channel to improve the user voice experience.


{% extends "home.html" %} {% load staticfiles %} {% block nav %}
In 2004, Alex Clark began doing business as (DBA) ACLARK.NET; a registered trade name in Maryland, USA. His first client was a company with a Plone website in London, UK.
In 2007, Amy Clark created ACLARK.NET, LLC; a limited liability corporation (LLC) in Maryland, USA. Our client list began to grow.
In 2008, Amy Clark created ZPUGDC, Inc; a non-profit 501(c)(3) corporation in Maryland, USA. With this organization we hosted Plone Conference 2008.
In 2014, we reached a milestone: 10 years in business.


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--- layout: default title: Dimerize, The GitHub Chronicles ---
Chugging along with GitHub and learning new, exciting things.
Not much here right now, I'll be showcasing some projects soon. Thanks!


hackGC is a weekend-long event where Grinnellians come together in teams to collaborate, innovate and build a piece of technology (Minimum Viable Product/Prototype) to help alleviate a social justice issue. Come brainstorm and implement solutions with us! No coding experience necessary!
As students at a small liberal arts college with an even smaller CS department, we're as aware as anybody else that there often seems to exist a "coder:non-coder" binary. Another purpose of hackGC, therefore, is to bridge that divide by offering a series of inspiring talks and workshops revolving around the intersection between social justice and technology, an excellent line-up of technical mentors, and an exhilarating hacking experience.
This event is sponsored by the Wilson Center for Innovation and Leadership.
Hackathon is like an “invention marathon”. Anyone who has an interest in technology attends a hackathon to learn, build & share their creations over the course of a weekend in a relaxed and welcoming atmosphere.
We welcome any Grinnell student! You don't have to major in CS.  You can come with a team, hack alone, or create a team. If you are hacking alone and want to find a team, we have many ways to help you find other participants to pair with!
According to our survey, about 70% of Grinnell students have never participate in a hackathon before. We encourage new programmers to come because hackathons provide an opportunity to gain experience. As a new programmer at hackGC, you will learn a lot in a short amount of time, be challenged, and build something awesome.
Nope! Before the event, you can create teams/join other teams here. We will also have a session after check in time to help people find team members, as well as a panel of guest speakers to help people think of ideas to work on for the hackathon. So you should sign up regardless!
There can be up to four people per team.
Website, mobile app, a game (text-based is fine!), statistical model, machine learning model, data visualization, a Shiny app, design sketch, or even just a well thought out idea! If you are wondering whether a piece of technology is eligible for hackGC, the answer is yes!
Unfortunately, no. Since this is the first year of hackGC, we cap the number of participants at 50. We contacted MLH and they said they are not interested in sponsoring events that have less than 100 participants. We have worked our hardest with the resources we have to bring you a comparable and unique experience.
Laptop chargers, phone chargers etc. Oh, and don't forget to bring friends, enthusiasm and willingness to challenge yourself!
No, but all your coding and work must be done at the site of the competition.
Definitely not! The main purpose of the event is to learn alot, collaborate with other Grinnellians and have fun. You will not get the most out of the experience if you are not fully awake and are exhausted throughout the event. Self-care is important!
No, participants are not allowed to work on their projects before the event. We WILL check this and will disqualify any teams/individuals who violate this. If you want to prepare for the hackathon, focus on gaining experience with and knowledge of the tools you hope to use to build your project.
Teams will demo their application, science fair style, to a panel of judges, who will deliberate on their favorite submissions to choose the winners.


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Console
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None
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Customizing UI Themes - Icons and UI Controls
A UI Theme is customized by adding information to the UI Theme description file that overrides the base (Light or Darcula) UI Theme.
Introduction to UI Theme Description File Syntax
The syntax of a Theme description file follows the JSON open-standard file format of key-value pairs. The minimum valid default file is the output of the DevKit Theme Wizard. Adding key-value pairs customizes a Theme.
UI Theme key-value pairs often use a color as the value
.
Colors are defined by six-digit RGB or eight-digit RGBA hexadecimal notation.
UI Theme Reference Implementations
When learning new syntax, it is often useful to have some existing implementations for reference. For example, refer to the Theme description file for the IntelliJ IDEA High Contrast Theme. It may also be helpful to review some of the UI Themes available at the JetBrains Plugin Repository.
Defining Named Colors
Colors can always be defined individually as six-digit RGB or eight-digit RGBA hexadecimal notation.
However, Theme definitions often use the same color in multiple places.
Maintaining a Theme is more manageable if Named Colors are globally defined in a colors {}
block as part of the *.theme.json
file.
After that, the Named Color can be used instead of a hexadecimal description of the color.
For example, defining the Named Color basicBackground
and then using it to set the background color for panels.
(Don’t be concerned with the "ui"
syntax in the example below, it will be discussed in Custom UI Control Colors.)
{
"name": "theme_basics",
"dark": false,
"author": "IntelliJ Platform SDK",
"editorScheme": "/Lightning.xml",
"colors": {
"basicBackground": "#E1E1E1"
},
"ui": {
"Panel.background": "basicBackground"
}
}
Customizing Icons
UI themes can customize the color of default IntelliJ IDEA UI icons, or substitute custom icons for the default ones.
Customization is done by adding an "icons": {}
section to the Theme description file.
Overriding the Global Color of Icons
Default global icon colors are customized by adding key-value pairs to a "ColorPalette": {}
section.
The ColorPalette
must be inserted in the icons
section.
In the following example the key
- the default red color (#DB5860) used for Action
icons in the Light Theme - is overridden to the value
of a different color (#D61A26):
{
"icons": {
"ColorPalette": {
"#DB5860": "#D61A26"
}
}
}
This color substitution is applied throughout the IDE UI.
Custom Icon Palette Colors
Icon Palettes are predefined UI Theme color keys, each describing a single color in an Actions
or Objects
context.
Icon Colors in “Actions” and “Objects” Contexts
IntelliJ IDEA has default icon colors defined for Actions
and Objects
contexts.
Actions
are Theme keys for icons that appear in the context of toolbars, and represent actions such as Compile, Run, or Debug.Objects
are Theme keys for icons that appear in the contexts of lists and trees, and represent entities like files, symbols, or run and debug configurations.
The JetBrains Platform UI Guideline for Icons
defines the default hexadecimal RGB values of colors for Actions
and Objects
keys.
Note that this document refers to Objects
keys as “Noun icons.”
Customizing “Actions” and “Objects” Icon Colors
An icon Palette color is customized by adding an Actions
or Objects
key
and custom color value
to the "ColorPalette": {}
section in a Theme description file.
The list of available icon Actions
and Objects
keys are provided by the completion popup in the editor:
For example, the following key-value pair changes the color for all blue-colored icons on toolbars to the color #5BC0DE:
{
"icons": {
"ColorPalette": {
"Actions.Blue": "#5BC0DE"
}
}
}
This more specific change to the Actions.Blue
color overrides the default definition.
It will also, in the narrower context of blue Actions
icons, supersede any global color overrides of the default blue icon color.
Custom Icons
The default IntelliJ IDEA UI icons can be replaced by custom icons. The file format for icons is SVG. The JetBrains Platform UI Guideline for Icons has detailed specifications for icons.
An icon replacement is described within the icon {}
section of a Theme description file.
Note that icon replacement key-value pairs appear outside of the ColorPalette
section.
For icon substitutions, the key
is the path to the default icon image.
This path is derived from the AllIcons.[Group].[IconName]
path in icon section reported by the UI Inspector.
For example, the Build (hammer) icon in the toolbar has the path Allcons.Actions.Compile
as reported by the UI Inspector.
Therefore the key
for the Build icon is /actions/compile.svg
.
The value
is the file name of the replacement icon, located in the resources
folder of the UI Theme plugin project:
{
"icons": {
"/actions/compile.svg": "/factory.svg"
}
}
The color of a replaced icon takes precedence over any ColorPalette
overrides.
Customizing UI Controls
UI Themes can change the appearance of more general controls in the IntelliJ IDEA UI. Examples of these controls are labels, buttons, checkboxes, trees, lists, and menus.
Custom UI Control Colors
The custom color of a UI control is specified by adding a key-value pair to the "ui": {}
section of a Theme description file.
A UI control key
has the compound format element.property
, where:
element
is the type (label, checkbox, etc.,) of the UI control.property
is how the color is applied. Examples includeforeground
,background
, anderrorForeground
.
Note that some UI control keys have more than two parts, for example Popup.Advertiser.foreground
or ScrollBar.Mac.Transparent.thumbColor
.
The full key must be used to customize that specific button control.
However, for other purposes the first section can be considered the element
, and the last section considered the property
.
Methods for finding UI control keys are in the Finding Attribute Keys for UI Controls section.
Customizing All UI Control Colors with the Same Property
All UI Controls that have the same property
portion of their key can be set to the same color.
This customization is done using the wildcard "*": {}
section in the Theme description file.
A key-value pair is inserted in this section, but only the property
portion of the key is specified.
The value
is the custom color.
The following example would change the default background color to #AED7E3 for all UI controls:
{
"ui": {
"*": {
"background": "#AED7E3"
}
}
}
Note that the wildcard "*": {}
section must be within the "ui": {}
section.
Customizing the Color of Specific UI Control Types
The color of a specific UI control types are changed by adding a key-value pair to the "ui": {}
section of a Theme description file.
The key
is the full element.property
format and the value
is the custom color.
The following example sets the background color for all labels to the color #F6E9C9
{
"ui": {
"*": {
"background": "#AED7E3"
},
"Label.background": "#F6E9C9"
}
}
The Label.background
entry supersedes, in the narrower context of label backgrounds, any default color as well as any wildcard color assigned to backgrounds.
Customizing the Color of UI Tabs
UI Tab colors are changed by key-value pairs in a Theme description file.
There are two implementations of tabs in the IntelliJ Platform:
- Editor Tabs, which e.g., represent open files in the Editor window, and in Tool Window bars.
- Tabbed Panes, which e.g., are used for the Run/Debug Configurations dialog.
The control keys for UI Tabs were expanded from release 2019.1 to 2019.2 of the IntelliJ Platform. The 2019.1 release control keys are compatible with release 2019.2 and later versions of the IntelliJ Platform.
| Release 2019.1 Element | Release 2019.2 Element | Description of Release 2019.2 Element |
|---|---|---|
| N/A | DefaultTabs |
Applied to all tabs except TabbedPane , unless overridden by a more specific Tab control element. |
EditorTabs |
EditorTabs |
Applied only to Editor tabs. Overrides any DefaultTab settings. 192 has many more property settings than 191. |
ToolWindow.HeaderTab |
ToolWindow.HeaderTab |
Applied only to Tool Window tabs. Overrides any DefaultTab settings. 192 has many more property settings than 191. |
DebuggerTabs |
DefaultTabs |
DefaultTab settings are used instead of DebuggerTabs , except for key DebuggerTabs.underlineHeight . |
TabbedPane |
TabbedPane |
Applied only to Tabbed Panes. |
Plugins.Tab |
TabbedPane |
Use TabbedPane instead. |
SearchEverywhere.Tab |
SearchEverywhere.Tab |
No change. |
Methods for identifying UI control keys are in the Finding Attribute Keys for UI Controls section.
For example, here is an excerpt from the IntelliJ Platform High Contrast Theme:
Note that a Theme file can mix versions of property
identifiers:
- The first three
property
entries are recognized by release 2019.1, and ignored by subsequent releases because they are defined by newproperty
identifiers. - The
underlineColor
property
is recognized by release 2019.1 and subsequent releases. - The
underlineHeight
property
was introduced in release 2019.2, and is ignored by previous releases. - The
underlinedTabBackground
property
was introduced in release 2019.2, replaces the 2019.1selectedBackground
, and is ignored by previous releases. - The
inactiveColoredFileBackground
property
was introduced in release 2019.2, replaces the 2019.1inactiveMaskColor
, and is ignored by previous releases.
{
"ui": {
"EditorTabs": {
"selectedForeground": "#FFFFFF",
"selectedBackground": "#0e5d73",
"inactiveMaskColor": "#000000FF",
"underlineColor": "#1AEBFF",
"underlineHeight": 4,
"underlinedTabBackground": "#000000",
"inactiveColoredFileBackground": "#00000000"
}
}
}
Customizing the Borders of UI Controls
The color and geometry of borders used in UI controls can be customized by key-value pairs in a Theme description file.
The format of keys for borders is element.property
, where:
element
is the type of UI control containing a border, such as a window or a popup menu.property
is the desired border appearance, for example:border
is the border width (in pixels) specified as top, left, bottom, and right widths. Border color is also (optionally) specified as hexadecimal RGB, e.g. “E6E6E6” with no “#” character.borderInsets
is the inset distance (in pixels) from the edge of theelement
to the border. It is specified as top, left, bottom, and right insets.
Methods for identifying UI control keys are in the Finding Attribute Keys for UI Controls section.
Customizing the Border Appearance of Specific UI Controls
The appearance of borders for specific UI control types are customized by adding a key-value pair to the "ui": {}
section of a Theme description file.
The following example sets a new border width and color for all windows:
{
"ui": {
"Window.border" : "4, 4, 4, 4, E6E6E6"
}
}
In this example the customized border supersedes the default definition and any global color override.
Finding Attribute Keys for UI Controls
There are hundreds of UI control element.property
keys defined in the IntelliJ Platform UI.
Some keys and strategies for applying them can be gleaned from the UI Theme reference implementations.
For a general search, here some suggested methods for locating UI control keys.
Finding a UI Control Key Using Code Completion in the Editor
The preferred method of finding UI control keys is to use the Code Completion feature in the IntelliJ IDEA editor.
Note that some keys presented by the code completion feature may be deprecated.
New entries in the "ui": {}
section will invoke the code completion popup, as shown below:
Beginning with version 2019.2 of the IntelliJ Platform, the editor has added features for Code Completion and Quick Documentation to show the release in which a UI control key began to be supported. It appears as the Since attribute in editor popups. In the Quick Documentation popup the format is e.g. Since: 2019.2. The Code Completion popup is similar, but it the format is e.g. [Since 2019.2].
Finding a UI Control Key using Laf Defaults UI
Using the Laf Defaults inspector, enter the element
portion of the key.
The Laf Defaults inspector will prompt with a list of UI Control keys and their default color.


{% extends path+"/../layout.html" %} {% block backlink %} Back {% endblock %} {% block leftcol %}
{% if data['upload-attempt'] == 1 %} {# Photo is too small #} {% elif data['upload-attempt'] == 2 %} {# Photo is too large #}Your photo will be automatically checked to make sure it's good enough.
Get more help to get your photo right
{% else %}Get more help to get your photo right
Your photo or scan will be automatically checked to make sure the image quality is good enough.
{% endif %}


Hello! You can call me Otto! My favorite snacks are Apples, Bananas, Pears, Cherries, and Oranges! I love to read and write stories!
I'm Paul! I Love Eggs, Avocado, Yogurt, Milk, and Granola! Math is my favorite subject and I like collecting bugs and stuff.
Howdy! I'm Cassy! I really like playing sports like soccer and volley ball. I like Turkey, Cheese, Bagels, Peanut Butter, and lots of water!
Hi! My name is Rock! My Favorite Foods are Asparagus, Squash, Mushrooms, Beats, Cabbage, and Peas! I enjoy running around with my friends in the forest!


Sharing cookies between applications.¶
Web sites commonly consist of many individual web applications, all working together harmoniously. If an application developer wants to provide a good single-sign-on experience, he’ll often need all of the different web applications within the site to share authentication tickets between each other.
To support this scenario, the data protection stack allows sharing Katana cookie authentication and ASP.NET 5 cookie authentication tickets.
Sharing authentication cookies between ASP.NET 5 applications.¶
To share authentication cookies between two different ASP.NET 5 applications, configure each application that should share cookies as follows.
- Install the package Microsoft.AspNet.Authentication.Cookies.Shareable into each of your ASP.NET 5 applications.
- In Startup.cs, locate the call to UseIdentity, which will generally look like the following.
// Add cookie-based authentication to the request pipeline.
app.UseIdentity();
- Remove the call to UseIdentity, replacing it with four separate calls to UseCookieAuthentication. (UseIdentity calls these four methods under the covers.) In the call to UseCookieAuthentication that sets up the application cookie, provide an instance of a DataProtectionProvider that has been initialized to a key storage location.
// Add cookie-based authentication to the request pipeline.
// NOTE: Need to decompose this into its constituent components
// app.UseIdentity();
app.UseCookieAuthentication(null, IdentityOptions.ExternalCookieAuthenticationScheme);
app.UseCookieAuthentication(null, IdentityOptions.TwoFactorRememberMeCookieAuthenticationScheme);
app.UseCookieAuthentication(null, IdentityOptions.TwoFactorUserIdCookieAuthenticationScheme);
app.UseCookieAuthentication(null, IdentityOptions.ApplicationCookieAuthenticationScheme,
dataProtectionProvider: new DataProtectionProvider(
new DirectoryInfo(@"c:\shared-auth-ticket-keys\")));
Caution: When used in this manner, the DirectoryInfo should point to a key storage location specifically set aside for authentication cookies. The application name is ignored (intentionally so, since you’re trying to get multiple applications to share payloads). You should consider configuring the DataProtectionProvider such that keys are encrypted at rest, as in the below example.
app.UseCookieAuthentication(null, IdentityOptions.ApplicationCookieAuthenticationScheme,
dataProtectionProvider: new DataProtectionProvider(
new DirectoryInfo(@"c:\shared-auth-ticket-keys\"),
configure =>
{
configure.ProtectKeysWithCertificate("thumbprint");
}));
The cookie authentication middleware will use the explicitly provided implementation of the DataProtectionProvider, which due to taking an explicit directory in its constructor is isolated from the data protection system used by other parts of the application.
Sharing authentication cookies between ASP.NET 4.x and ASP.NET 5 applications.¶
ASP.NET 4.x applications which use Katana cookie authentication middleware can be configured to generate authentication cookies which are compatible with the ASP.NET 5 cookie authentication middleware. This allows upgrading a large site’s individual applications piecemeal while still providing a smooth single sign on experience across the site.
Tip: You can tell if your existing application uses Katana cookie authentication middleware by the existence of a call to UseCookieAuthentication in your project’s Startup.Auth.cs. ASP.NET 4.x web application projects created with Visual Studio 2013 and later use the Katana cookie authentication middleware by default.
Note
Your ASP.NET 4.x application must target .NET Framework 4.5.1 or higher, otherwise the necessary NuGet packages will fail to install.
To share authentication cookies between your ASP.NET 4.x applications and your ASP.NET 5 applications, configure the ASP.NET 5 application as stated above, then configure your ASP.NET 4.x applications by following the steps below.
- Install the package Microsoft.Owin.Security.Cookies.Shareable into each of your ASP.NET 4.x applications.
- In Startup.Auth.cs, locate the call to UseCookieAuthentication, which will generally look like the following.
app.UseCookieAuthentication(new CookieAuthenticationOptions
{
// ...
});
- Modify the call to UseCookieAuthentication as follows, changing the AuthenticationType and CookieName to match those of the ASP.NET 5 cookie authentication middleware, and providing an instance of a DataProtectionProvider that has been initialized to a key storage location.
app.UseCookieAuthentication(new CookieAuthenticationOptions
{
AuthenticationType = DefaultCompatibilityConstants.ApplicationCookieAuthenticationType,
CookieName = DefaultCompatibilityConstants.CookieName,
// CookiePath = "...", (if necessary)
// ...
},
dataProtectionProvider: new DataProtectionProvider(
new DirectoryInfo(@"c:\shared-auth-ticket-keys\")));
The DirectoryInfo has to point to the same storage location that you pointed your ASP.NET 5 application to and should be configured using the same settings.
- In IdentityModels.cs, change the call to ApplicationUserManager.CreateIdentity to use the same authentication type as in the cookie middleware.
public ClaimsIdentity GenerateUserIdentity(ApplicationUserManager manager)
{
// Note the authenticationType must match the one defined in CookieAuthenticationOptions.AuthenticationType
var userIdentity = manager.CreateIdentity(this, DefaultCompatibilityConstants.ApplicationCookieAuthenticationType);
// ...
}
The ASP.NET 4.x and ASP.NET 5 applications are now configured to share authentication cookies.
Note
You’ll need to make sure that the ASP.NET Identity system for each application is pointed at the same user database. Otherwise the identity system will produce failures at runtime when it tries to match the information in the authentication cookie against the information in its database.


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VolumeBar
VolumeBar is a Swift volume indicator that doesn’t obstruct content on screen.
| Features | |
|---|---|
| :no_good: | Hides system volume HUD automatically |
| :art: | Customizable appearance with presets |
| :boom: | Support for custom animations |
| :iphone: | Works with iPhone X |
| :books: | Fully documented |
| :baby_chick: | Swift 4 |
Usage
It’s super easy to add VolumeBar to your app:
let volumeBar = VolumeBar.shared
volumeBar.style = .likeInstagram
volumeBar.start()
Customize appearance attributes (see VolumeBarStyle
):
let volumeBar = VolumeBar.shared
let customStyle = VolumeBarStyle.likeInstagram
customStyle.trackTintColor = .white
customStyle.trackTintColor = .darkGray
customStyle.backgroundColor = .black
volumeBar.style = customStyle
Or even use custom animations (see VolumeBarAnimation
):
let volumeBar = VolumeBar.shared
let fadeInAnimation = VolumeBarAnimation({ (view, completion) in
view.alpha = 0
UIView.animate(withDuration: 0.2, animations: {
view.alpha = 1
}, completion: completion)
})
volumeBar.showAnimation = fadeInAnimation
Background Audio
If your app doesn’t do custom audio handling, adding VolumeBar will make background music (like Spotify) pause when your app is opened.
Prevent this by adding the following wherever you call VolumeBar.shared.start()
:
try! AVAudioSession.sharedInstance().setCategory(AVAudioSessionCategoryAmbient)
VolumeBar
VolumeBar is fully documented here.
Installation
CocoaPods
source 'https://github.com/CocoaPods/Specs.git'
use_frameworks!
pod 'VolumeBar', '~> 2.0.6'
Carthage
github "gizmosachin/VolumeBar" "master"
Sample
Please see the Sample
directory for a basic iOS project that uses VolumeBar
.
Contributing
VolumeBar is a community - contributions and discussions are welcome!
Please read the contributing guidelines prior to submitting a Pull Request.
License
VolumeBar is available under the MIT license, see the LICENSE file for more information.


DBMS | Database Web and Development | Database Warehousing, Mining and Visualization | IS Design and Development| IS Project and Change Management| UIUX| Marketing Research | Bigdata| Visual Design to Technology
I was responsible for gathering and documenting business requirements. I was mainly engaged in communicating with the stakeholder and delivering results are expected. Over the course of time, I have developed my critical thinking and I believe that I have strong communication skills which are the major requirement for any job. I have experience of working in the team and delivering milestones on time.
Managed customer information database and changed schema design to improve performance and assisted in data gathering and analysis of data with SDLC Methology
GPA: 3.6
Percentage: 83%
Percentage: 70%
Percentage: 70%
Utilized Tableau for data exploration to understand dive deeper into the data and look for patterns and created dashboard reports on how different markets affect various customer segments
Built charter using MS Project and Visio by defining goals, objectives, assumptions, and risks to improve systems. Evaluated a project plan by establishing a Work Break Down Structure to estimate budget
Performed data cleaning, imputed missing values, normalization and scaling to create a concise and clean dataset using R. Executed KNN classification clustering to different segments of buyers and tested regression model to each category to find it out accuracy of model Technology: R | Tools: R-Studio | libraries: Tidy verse, gg plot
Conducted research and created personas, user-flows, scenarios, wireframes numerous prototypes of varying fidelity for usability testing and findings. Designed and developed a mobile application for user with the help of Sketch and OmniGraffle


From:Geaccone To:Moore Sent:2017-01-11T04:38:26.0000000Z Subject:FW: Red Rock additions
-----Original Message-----
From: Hayslett, Rod
Sent: Monday, November 26, 2001 11:23 AM
To: Geaccone, Tracy
Subject: FW: Red Rock additions
Importance: High
FYYI
-----Original Message-----
From: Taylor, Sarah
Sent: Monday, November 26, 2001 11:21 AM
To: Hayslett, Rod
Subject: FW: Red Rock additions
Importance: High
-----Original Message-----
From: Hayslett, Rod
Sent: Sunday, November 25, 2001 3:18 PM
To: Taylor, Sarah<EMAIL_ADDRESS>Cc<EMAIL_ADDRESS>Desai, Jayshree
Subject: RE: Red Rock additions
Importance: High
FYI. This is my story for now, but I think it explains the volumes and the rates as well as the revenue projections. Please note we have found a bust in 2002 revenue. This yields a higher answer without any additional volumes being used.
-----Original Message-----
From: Taylor, Sarah
Sent: Sun 11/25/2001 3:04 PM
To: Hayslett, Rod<EMAIL_ADDRESS>Cc<EMAIL_ADDRESS>Desai, Jayshree
Subject: Red Rock additions
<<Exisiting capacity projections w. Red Rock.xls>>
***********
EDRM Enron Email Data Set has been produced in EML, PST and NSF format by ZL Technologies, Inc. This Data Set is licensed under a Creative Commons Attribution 3.0 United States License <http://creativecommons.org/licenses/by/3.0/us/> . To provide attribution, please cite to "ZL Technologies, Inc. (http://www.zlti.com)."
***********
California


| Year and model: | 2013 SLK 200 R172. |
|---|---|
| Engine: | 1.8 L 135 kW (184 PS; 181 hp) I4 turbocharged. |
| Transmission: | 7 speeds AMG Sports 7G-TRONIC-PLUS automatic and tiptronic, with controls behind the steering wheel. |
| Top speed: | 240 km/h (according to Mercedes data; achieved a little more on German autobahns). |
| Suspension: | "Dynamic handling" and "AMG Sports" packages : there is a button to switch between "Comfort" and "Sports" modes. In "Sports", the car will be slightly lower, the suspension will be harder and the steering and accelerator responsiveness increases. You can have a very rewarding drive on the road that only a real sportscar can offer, and a comfortable, soft drive in the city. |
| Safety: | PRE-SAFE System (the car identifies near-crash situations and tightens the seat belts); Pedestrian protection (raises the hood to protect a pedestrian from hitting the windshield); tire pressure loss warning; heated windscreen washing; plus all high-standard Mercedes-Benz safety systems: multiple air-bags, stability controls, etc. |
| Roof: | Glass hard-top "vario-roof" offers superb acoustic isolation. Opening and closing the roof is very simple: the system is fully automatic, so you just need to push a button and the roof will retract to the trunk. There will still be plenty of room for luggage, even with the roof open! |
| Interior design: | AMG Sports package: interior styling in aluminum and black leather with red stitches and seat belts. Interior and ambient lighting packages with feature red light bars. "Mercedes-Benz" aluminum door sill. This car has been ordered directly from the Mercedes factory in Bremen and all design options have been carefully chosen by the owner, so it is unlikely to find a copy in Kyiv. |
| Body design: | All features of the AMG Sports body styling package: aluminum roll over bars, air inlets, special exhausts, 18" wheels and more. The car looks very unique: it is bold, beautiful and classy. |
| Comfort options: | Mirror package: automatic dimming of mirrors and folding; AIRGUIDE transparent frame for reducing the wind on the road, with the roof open; AIRSCARF: will blow warm air behind your neck, so that you can open the roof even on cold days; Automatic windscreen wiper with rain sensor; Media center with Bluetooth telephony; THERMOTRONIC automatic air conditioning; Heated seats; plus all amenities you would expect from a Mercedes. |
| Status: | The car is in great condition. Smoking and eating has never been allowed inside. All yearly maintenance has been made at the Mercedes-Benz "Dim Ukraina" dealership. Has travelled 26600 km, mainly on road trips in Europe. |
| Price: | Will sell for US$ 39,900. Customs have not been cleared. |


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LogicCircuit
whose boolean
value is under public control.LogicCircuit
they
are registered with when it begins the proces of changing its boolean
value, and when it ends that process.ManyInputs.addInput(LogicCircuit)
when
ManyInputs.addInput(LogicCircuit)
when
ManyInputs.updateValue()
to do the actual
recalculation of the boolean value.
LogicGate
s with
many inputs.RepresentationCanvas
.LogicCircuit
s LogicCircuit
(see LogicCircuit.getValue()
).LogicCircuit
.LogicCircuit
LogicCircuit
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--- title: 'Normalization results in regression to the mean and inflated Type I error conditional on the reference values' author: Jeff Walker date: '2019-10-16' slug: normalization-results-in-regression-to-the-mean categories: - reproducibility - stats 101 tags: - ancova - effect size - fake data - regression to the mean - bias - normalization keywords: - tech ---
Fig 1C of the Replication Study: Melanoma exosomes educate bone marrow progenitor cells toward a pro-metastatic phenotype through MET uses an odd (to me) three stage normalization procedure for the quantified western blots. The authors compared blot values between a treatment (shMet cells) and a control (shScr cells) using GAPDH to normalize the values. The three stages of the normalization are
As shown in the simulation below and summarized in the section [Summary of simulation results for n=4], Stage 1 can introduce inflated conditional type I error due to regression to the mean while stage 2 and 3 renormalizations introduce inflated marginal (or unconditional) type I error.


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