Crispulator.jl: Pooled CRISPR Screen Optimization tool

CRISPulator

A pooled genetic screen simulator

Crispulator does not yet support Julia 1.0! We're still waiting on all the dependencies to be updated, please use Julia v0.6.4 in the mean time.

Motivation

Pooled screens are very useful, but they are also extraordinarily complex. This work aims to explore the importance of various screen parameters and the relevance of design choices on the downstream analysis and interpretation.

Paper

Nagy, T. & Kampmann, M. CRISPulator: a discrete simulation tool for pooled genetic screens. BMC Bioinformatics 18, 347 (2017). https://doi.org/10.1186/s12859-017-1759-9 (Preprint also available)

Documentation

  • STABLEmost recently tagged version of the documentation.
  • LATESTin-development version of the documentation.

Download Details:

Author: tlnagy
Source Code: https://github.com/tlnagy/Crispulator.jl 
License: View license

#julia #functional 

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Crispulator.jl: Pooled CRISPR Screen Optimization tool
Sean Wade

Sean Wade

1657785244

How to Create a Custom Video Player with HTML, CSS & Javascript

Create a custom video player using HTML, CSS and Javascript.

In today’s tutorial, we will learn how to create a Custom Video Player. To build this project, we need HTML, CSS and Javascript.

00:00 Intro
00:05 Preview
02:58 HTML & CSS
35:26 Step 1: Create Initial References
45:46 Step 2: Implement slider() For Volume
51:33 Step 3: Detect Device Type
57:27 Step 4: Implement Functionality For Play & Pause Button
01:03:04 Step 5: Hide/ Show Playback Speed Options
01:08:47 Step 6: Function To Set Playback Speed.
01:12:59 Step 7: Function To Mute Video
01:18:24 Step 8: Function To Set Volume
01:24:55 Step 9: Function To Set Fullscreen
01:31:47 Step 10: Function To Exit Fullscreen
01:40:08 Step 11: Function To Format Current Time & Total Time
01:44:46 Step 12: Function To Update Progress & Timer
01:50:13 Step 13: Implement Click Event On Progress Bar
01:57:26 Step 14: Function On Window Load


Project Folder Structure:

Before we start coding let us take a look at the project folder structure. We create a project folder called – ‘Custom Video Player’. Inside this folder, we have three files. The first file is index.html which is the HTML document. Next, we have style.css which is the stylesheet. Finally, we have script.js which is the script file.

HTML:

We start with the HTML code. First, copy the code below and paste it into your HTML document.

<!DOCTYPE html>
<html lang="en">
  <head>
    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
    <title>Custom Video Player</title>
    <!-- Font Awesome Icons -->
    <link
      rel="stylesheet"
      href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.1.1/css/all.min.css"
    />
    <!-- Google Fonts -->
    <link
      href="https://fonts.googleapis.com/css2?family=Roboto+Mono&display=swap"
      rel="stylesheet"
    />
    <!-- Stylesheet -->
    <link rel="stylesheet" href="style.css" />
  </head>
  <body>
    <div class="container">
      <div class="rotate-container hide">
        <div id="rotate-icon">
          <i class="fa-solid fa-rotate-left"></i>
          <p>Rotate for a better experience</p>
        </div>
      </div>
      <div class="video-container" id="video-container">
        <video id="my-video" preload="metadata">
          <source
            src="https://dl.dropbox.com/s/l90y72zm97ayzhx/my%20video.mp4?raw=1"
            type="video/mp4"
          />
          Your browser does not support the video tag
        </video>
        <div class="controls" id="controls">
          <div class="progress-container flex-space">
            <div id="progress-bar">
              <div id="current-progress"></div>
            </div>
            <div class="song-timer">
              <span id="current-time">00:00</span>
              <span>/</span>
              <span id="max-duration">00:00</span>
            </div>
          </div>
          <div id="video-controls" class="video-controls flex-space">
            <div class="container-1 flex">
              <div>
                <!-- Play video -->
                <button id="play-btn" class="control-btn">
                  <i class="fa-solid fa-play"></i>
                </button>
                <!-- Pause video-->
                <button id="pauseButton" class="control-btn hide">
                  <i class="fa-solid fa-pause"></i>
                </button>
              </div>
              <!-- volume of video-->
              <div id="volume" class="volume flex">
                <span id="high">
                  <i class="fa-solid fa-volume-high"></i>
                </span>
                <span class="hide" id="low">
                  <i class="fa-solid fa-volume-low"></i>
                </span>
                <span class="hide" id="mute">
                  <i class="fa-solid fa-volume-xmark"></i>
                </span>
                <input
                  type="range"
                  min="0"
                  max="100"
                  value="50"
                  id="volume-range"
                  oninput="slider()"
                />
                <span id="volume-num">50</span>
              </div>
            </div>
            <div class="container-2 flex-space">
              <div class="playback">
                <button id="playback-speed-btn">1x</button>
                <div class="playback-options hide">
                  <button onclick="setPlayback(0.5)">0.5</button>
                  <button onclick="setPlayback(1.0)">1</button>
                  <button onclick="setPlayback(2.0)">2</button>
                </div>
              </div>
              <!-- screen size -->
              <div id="size-screen">
                <button id="screen-expand">
                  <i class="fa-solid fa-expand"></i>
                </button>
                <button id="screen-compress" class="hide">
                  <i class="fa-solid fa-compress"></i>
                </button>
              </div>
            </div>
          </div>
        </div>
      </div>
    </div>
    <!-- Script -->
    <script src="script.js"></script>
  </body>
</html>

CSS:

Next, we style our video player using CSS. For this copy, the code provided to you below and paste it into your stylesheet.

* {
  padding: 0;
  margin: 0;
  box-sizing: border-box;
  outline: none;
  color: #ffffff;
  font-family: "Roboto Mono", monospace;
}
body {
  background-color: #2887e3;
}
.flex {
  display: flex;
}
.flex-space {
  display: flex;
  justify-content: space-between;
}
.container {
  padding: 1em 0;
}
#my-video {
  width: 100%;
}
.rotate-container {
  top: 0;
  position: absolute;
  height: 100%;
  width: 100%;
  background-color: rgba(0, 0, 0, 0.3);
  display: flex;
  justify-content: center;
  align-items: center;
}
#rotate-icon {
  display: flex;
  flex-direction: column;
  color: #dddddd;
  text-align: center;
}
.hide {
  display: none;
}
.video-container {
  width: 60%;
  position: absolute;
  transform: translate(-50%, -50%);
  left: 50%;
  top: 50%;
  box-shadow: 20px 30px 50px rgba(0, 0, 0, 0.2);
}
.controls {
  position: absolute;
  left: 0;
  right: 0;
  bottom: 0;
  background-color: rgba(35, 34, 39, 0.8);
}
.progress-container {
  align-items: center;
  padding: 0 0.5em;
}
.video-controls {
  flex-direction: row;
  align-items: center;
}
#progress-bar {
  position: relative;
  width: 75%;
  height: 5px;
  background-color: #000000;
  margin: 1em 0;
  vertical-align: 2px;
  border-radius: 5px;
  cursor: pointer;
}
.song-timer {
  font-size: 0.8em;
  width: 25%;
  text-align: right;
}
#current-progress {
  position: absolute;
  left: 0;
  display: inline-block;
  height: 5px;
  width: 0;
  background: #2887e3;
  border-radius: 5px;
}
#current-progress:after {
  content: "";
  position: absolute;
  left: calc(100% - 1.5px);
  top: -2.5px;
  width: 10px;
  height: 10px;
  border-radius: 50%;
  background-color: #ffffff;
}
.playback {
  position: relative;
}
.control-btn,
#screen-expand,
#screen-compress {
  width: 3em;
  height: 3em;
  outline: none;
  border: none;
  background-color: transparent;
}
#size-screen {
  margin-left: auto;
}
.volume {
  align-items: center;
  margin-left: 0.6em;
}
#volume-range {
  position: relative;
  margin: 0 0.5em;
  cursor: pointer;
  height: 5px;
  -webkit-appearance: none;
  background-color: #000000;
  border-radius: 5px;
  outline: none;
}
input[type="range"]::-webkit-slider-thumb {
  -webkit-appearance: none;
  height: 10px;
  width: 10px;
  background-color: #2887e3;
  border-radius: 50%;
  cursor: pointer;
  border: none;
}
.fa-solid {
  font-size: 1.1rem;
}
.container-2 {
  width: 10%;
  min-width: 70px;
  align-items: center;
}
#playback-speed-btn {
  position: relative;
  background-color: transparent;
  border: 1px solid #ffffff;
  color: #ffffff;
  font-size: 0.9rem;
  border-radius: 5px;
  padding: 0.3em 0.25em;
  cursor: pointer;
}
.playback-options {
  position: absolute;
  bottom: 0;
  background-color: #000000;
  min-width: 5em;
  box-shadow: 0 8px 16px 0 rgba(0, 0, 0, 0.2);
  z-index: 1;
}
.playback-options button {
  color: #ffffff;
  border-left: 0;
  border-right: 0;
  border-top: 0;
  width: 100%;
  background-color: transparent;
  padding: 1em;
  text-decoration: none;
  display: block;
}
@media all and (display-mode: fullscreen) {
  .container {
    padding: 0;
  }
  .video-container {
    width: 100%;
    margin: 0;
  }
  .controls {
    position: absolute;
    display: block;
    bottom: 0;
    left: 0;
    width: 100%;
    z-index: 2;
  }
  #progress-bar {
    width: 80%;
  }
  .song-timer {
    width: 20%;
    font-size: 1.2em;
  }
  .fa-solid {
    color: #dddddd;
  }
}

@media only screen and (max-width: 768px) {
  .video-container,
  .controls {
    width: 100%;
  }
  span {
    display: inline;
  }
  #progress-bar {
    width: 60%;
  }
  .song-timer {
    width: 40%;
    font-size: 0.9em;
  }
  .fa-solid {
    font-size: 1rem;
  }
  .control-btn,
  #screen-expand,
  #screen-compress {
    width: 2em;
    height: 1.5em;
  }
}
@media only screen and (max-width: 768px) and (display-mode: fullscreen) {
  .video-container {
    margin-top: 50%;
  }
}

Javascript:

Lastly, we add functionality to our custom video player using Javascript. Once again copy the code below and paste it into your script file.
We do this in fourteen steps:
Create initial references.
Implement slider()
Detect device type.
Implement functionality for the play and pause button.
Hide/Show playback speed options
Function to set playback speed.
Logic to mute video.
Function to set Fullscreen.
Function to exit Fullscreen.
Create a function to format the current time & maximum time.
Create a function to update progress & timer.
Implement a click event on the progress bar.
Function on window load.

let videoContainer = document.querySelector(".video-container");
let container = document.querySelector(".container");
let myVideo = document.getElementById("my-video");
let rotateContainer = document.querySelector(".rotate-container");
let videoControls = document.querySelector(".controls");
let playButton = document.getElementById("play-btn");
let pauseButton = document.getElementById("pauseButton");
let volume = document.getElementById("volume");
let volumeRange = document.getElementById("volume-range");
let volumeNum = document.getElementById("volume-num");
let high = document.getElementById("high");
let low = document.getElementById("low");
let mute = document.getElementById("mute");
let sizeScreen = document.getElementById("size-screen");
let screenCompress = document.getElementById("screen-compress");
let screenExpand = document.getElementById("screen-expand");
const currentProgress = document.getElementById("current-progress");
const currentTimeRef = document.getElementById("current-time");
const maxDuration = document.getElementById("max-duration");
const progressBar = document.getElementById("progress-bar");
const playbackSpeedButton = document.getElementById("playback-speed-btn");
const playbackContainer = document.querySelector(".playback");
const playbackSpeedOptions = document.querySelector(".playback-options");

function slider() {
  valPercent = (volumeRange.value / volumeRange.max) * 100;
  volumeRange.style.background = `linear-gradient(to right, #2887e3 ${valPercent}%, #000000 ${valPercent}%)`;
}

//events object
let events = {
  mouse: {
    click: "click",
  },
  touch: {
    click: "touchstart",
  },
};

let deviceType = "";

//Detech touch device
const isTouchDevice = () => {
  try {
    //We try to create TouchEvent (it would fail for desktops and throw error)
    document.createEvent("TouchEvent");
    deviceType = "touch";
    return true;
  } catch (e) {
    deviceType = "mouse";
    return false;
  }
};

//play and pause button
playButton.addEventListener("click", () => {
  myVideo.play();
  pauseButton.classList.remove("hide");
  playButton.classList.add("hide");
});

pauseButton.addEventListener(
  "click",
  (pauseVideo = () => {
    myVideo.pause();
    pauseButton.classList.add("hide");
    playButton.classList.remove("hide");
  })
);

//playback
playbackContainer.addEventListener("click", () => {
  playbackSpeedOptions.classList.remove("hide");
});

//if user clicks outside or on the option
window.addEventListener("click", (e) => {
  if (!playbackContainer.contains(e.target)) {
    playbackSpeedOptions.classList.add("hide");
  } else if (playbackSpeedOptions.contains(e.target)) {
    playbackSpeedOptions.classList.add("hide");
  }
});

//playback speed
const setPlayback = (value) => {
  playbackSpeedButton.innerText = value + "x";
  myVideo.playbackRate = value;
};

//mute video
const muter = () => {
  mute.classList.remove("hide");
  high.classList.add("hide");
  low.classList.add("hide");
  myVideo.volume = 0;
  volumeNum.innerHTML = 0;
  volumeRange.value = 0;
  slider();
};

//when user click on high and low volume then mute the audio
high.addEventListener("click", muter);
low.addEventListener("click", muter);

//for volume
volumeRange.addEventListener("input", () => {
  //for converting % to decimal values since video.volume would accept decimals only
  let volumeValue = volumeRange.value / 100;
  myVideo.volume = volumeValue;
  volumeNum.innerHTML = volumeRange.value;
  //mute icon, low volume, high volume icons
  if (volumeRange.value < 50) {
    low.classList.remove("hide");
    high.classList.add("hide");
    mute.classList.add("hide");
  } else if (volumeRange.value > 50) {
    low.classList.add("hide");
    high.classList.remove("hide");
    mute.classList.add("hide");
  }
});

//Screen size
screenExpand.addEventListener("click", () => {
  screenCompress.classList.remove("hide");
  screenExpand.classList.add("hide");
  videoContainer
    .requestFullscreen()
    .catch((err) => alert("Your device doesn't support full screen API"));
  if (isTouchDevice) {
    let screenOrientation =
      screen.orientation || screen.mozOrientation || screen.msOrientation;
    if (screenOrientation.type == "portrait-primary") {
      //update styling for fullscreen
      pauseVideo();
      rotateContainer.classList.remove("hide");
      const myTimeout = setTimeout(() => {
        rotateContainer.classList.add("hide");
      }, 3000);
    }
  }
});

//if user presses escape the browser fire 'fullscreenchange' event
document.addEventListener("fullscreenchange", exitHandler);
document.addEventListener("webkitfullscreenchange", exitHandler);
document.addEventListener("mozfullscreenchange", exitHandler);
document.addEventListener("MSFullscreenchange", exitHandler);

function exitHandler() {
  //if fullscreen is closed
  if (
    !document.fullscreenElement &&
    !document.webkitIsFullScreen &&
    !document.mozFullScreen &&
    !document.msFullscreenElement
  ) {
    normalScreen();
  }
}

//back to normal screen
screenCompress.addEventListener(
  "click",
  (normalScreen = () => {
    screenCompress.classList.add("hide");
    screenExpand.classList.remove("hide");
    if (document.fullscreenElement) {
      if (document.exitFullscreen) {
        document.exitFullscreen();
      } else if (document.mozCancelFullScreen) {
        document.mozCancelFullScreen();
      } else if (document.webkitExitFullscreen) {
        document.webkitExitFullscreen();
      }
    }
  })
);

//Format time
const timeFormatter = (timeInput) => {
  let minute = Math.floor(timeInput / 60);
  minute = minute < 10 ? "0" + minute : minute;
  let second = Math.floor(timeInput % 60);
  second = second < 10 ? "0" + second : second;
  return `${minute}:${second}`;
};

//Update progress every second
setInterval(() => {
  currentTimeRef.innerHTML = timeFormatter(myVideo.currentTime);
  currentProgress.style.width =
    (myVideo.currentTime / myVideo.duration.toFixed(3)) * 100 + "%";
}, 1000);

//update timer
myVideo.addEventListener("timeupdate", () => {
  currentTimeRef.innerText = timeFormatter(myVideo.currentTime);
});

//If user click on progress bar
isTouchDevice();
progressBar.addEventListener(events[deviceType].click, (event) => {
  //start of progressbar
  let coordStart = progressBar.getBoundingClientRect().left;
  //mouse click position
  let coordEnd = !isTouchDevice() ? event.clientX : event.touches[0].clientX;
  let progress = (coordEnd - coordStart) / progressBar.offsetWidth;
  //set width to progress
  currentProgress.style.width = progress * 100 + "%";
  //set time
  myVideo.currentTime = progress * myVideo.duration;
  //play
  myVideo.play();
  pauseButton.classList.remove("hide");
  playButton.classList.add("hide");
});

window.onload = () => {
  //display duration
  myVideo.onloadedmetadata = () => {
    maxDuration.innerText = timeFormatter(myVideo.duration);
  };
  slider();
};

That’s it for this tutorial. If you face any issues while creating this code, you can download the source code by clicking the ‘Download Code’ 

📁 Download Source Code : https://www.codingartistweb.com

#html #css #javascript #webdev 

Arvel  Parker

Arvel Parker

1591627260

How to Use the Screen Command in Linux

Screen is a terminal program in Linux which allows us to use a virtual (VT100 terminal) as full-screen window manager which multiplexes an open physical terminal between multiple processes, which are typically, interactive shells. It allows us to access multiple terminal sessions within a single terminal or a remote terminal session. It is most useful when addressing multiple Linux shell commands on the command line, as well as separating commands from the shell that started the commands.

Screen also allows a user to initiate a command from one terminal, disconnect from that terminal, and then reconnect from a different location to that same terminal, while using a different terminal without having to restart the command. This simply lets a user better control multiple and separate command windows.

Screen also lets multiple remote computers connect to the same screen session at once. This allows multiple users to connect to the same screen session allowing a second user to follow along with another administrator working on a server.

#tutorials #attach #cli #command line #detach #key bindings #logging #multiplex #multiuser #multiuser mode #remote access #remote management #remote session #remote terminal #screen #screen logging #screen session #screenlog #screens #scrollback #shell #terminal #terminal session #terminal window #tty #vt100

Crispulator.jl: Pooled CRISPR Screen Optimization tool

CRISPulator

A pooled genetic screen simulator

Crispulator does not yet support Julia 1.0! We're still waiting on all the dependencies to be updated, please use Julia v0.6.4 in the mean time.

Motivation

Pooled screens are very useful, but they are also extraordinarily complex. This work aims to explore the importance of various screen parameters and the relevance of design choices on the downstream analysis and interpretation.

Paper

Nagy, T. & Kampmann, M. CRISPulator: a discrete simulation tool for pooled genetic screens. BMC Bioinformatics 18, 347 (2017). https://doi.org/10.1186/s12859-017-1759-9 (Preprint also available)

Documentation

  • STABLEmost recently tagged version of the documentation.
  • LATESTin-development version of the documentation.

Download Details:

Author: tlnagy
Source Code: https://github.com/tlnagy/Crispulator.jl 
License: View license

#julia #functional 

50+ Useful DevOps Tools

The article comprises both very well established tools for those who are new to the DevOps methodology.

What Is DevOps?

The DevOps methodology, a software and team management approach defined by the portmanteau of Development and Operations, was first coined in 2009 and has since become a buzzword concept in the IT field.

DevOps has come to mean many things to each individual who uses the term as DevOps is not a singularly defined standard, software, or process but more of a culture. Gartner defines DevOps as:

“DevOps represents a change in IT culture, focusing on rapid IT service delivery through the adoption of agile, lean practices in the context of a system-oriented approach. DevOps emphasizes people (and culture), and seeks to improve collaboration between operations and development teams. DevOps implementations utilize technology — especially automation tools that can leverage an increasingly programmable and dynamic infrastructure from a life cycle perspective.”

As you can see from the above definition, DevOps is a multi-faceted approach to the Software Development Life Cycle (SDLC), but its main underlying strength is how it leverages technology and software to streamline this process. So with the right approach to DevOps, notably adopting its philosophies of co-operation and implementing the right tools, your business can increase deployment frequency by a factor of 30 and lead times by a factor of 8000 over traditional methods, according to a CapGemini survey.

The Right Tools for the Job

This list is designed to be as comprehensive as possible. The article comprises both very well established tools for those who are new to the DevOps methodology and those tools that are more recent releases to the market — either way, there is bound to be a tool on here that can be an asset for you and your business. For those who already live and breathe DevOps, we hope you find something that will assist you in your growing enterprise.

With such a litany of tools to choose from, there is no “right” answer to what tools you should adopt. No single tool will cover all your needs and will be deployed across a variety of development and Operational teams, so let’s break down what you need to consider before choosing what tool might work for you.

  • Plan and collaborate: Before you even begin the SDLC, your business needs to have a cohesive idea of what tools they’ll need to implement across your teams. There are even DevOps tools that can assist you with this first crucial step.
  • Build: Here you want tools that create identically provisioned environments. The last you need is to hear “But it works for me on my computer”
  • Automation: This has quickly become a given in DevOps, but automation will always drastically increase production over manual methods.
  • Continuous Integration: Tools need to provide constant and immediate feedback, several times a day but not all integrations are implemented equally, will the tool you select be right for the job?
  • Deployment: Deployments need to be kept predictable, smooth, and reliable with minimal risks, automation will also play a big part in this process.

With all that in mind, I hope this selection of tools will aid you as your business continues to expand into the DevOps lifestyle.

Tools Categories List:

Infrastructure As Code

Continuous Integration and Delivery

Development Automation

Usability Testing

Database and Big Data

Monitoring

Testing

Security

Helpful CLI Tools

Development

Visualization

Infrastructure As Code

#AWSCloudFormation

1. AWS CloudFormation

AWS CloudFormation is an absolute must if you are currently working, or planning to work, in the AWS Cloud. CloudFormation allows you to model your AWS infrastructure and provision all your AWS resources swiftly and easily. All of this is done within a JSON or YAML template file and the service comes with a variety of automation features ensuring your deployments will be predictable, reliable, and manageable.

Link: https://aws.amazon.com/cloudformation/

2. Azure Resource Manager

Azure Resource Manager (ARM) is Microsoft’s answer to an all-encompassing IAC tool. With its ARM templates, described within JSON files, Azure Resource Manager will provision your infrastructure, handle dependencies, and declare multiple resources via a single template.

Link: https://azure.microsoft.com/en-us/features/resource-manager/

#Google Cloud Deployment Manager

3. Google Cloud Deployment Manager

Much like the tools mentioned above, Google Cloud Deployment Manager is Google’s IAC tool for the Google Cloud Platform. This tool utilizes YAML for its config files and JINJA2 or PYTHON for its templates. Some of its notable features are synchronistic deployment and ‘preview’, allowing you an overhead view of changes before they are committed.

Link: https://cloud.google.com/deployment-manager/

4. Terraform

Terraform is brought to you by HashiCorp, the makers of Vault and Nomad. Terraform is vastly different from the above-mentioned tools in that it is not restricted to a specific cloud environment, this comes with increased benefits for tackling complex distributed applications without being tied to a single platform. And much like Google Cloud Deployment Manager, Terraform also has a preview feature.

Link: https://www.terraform.io/

#Chef

5. Chef

Chef is an ideal choice for those who favor CI/CD. At its heart, Chef utilizes self-described recipes, templates, and cookbooks; a collection of ready-made templates. Cookbooks allow for consistent configuration even as your infrastructure rapidly scales. All of this is wrapped up in a beautiful Ruby-based DSL pie.

Link: https://www.chef.io/products/chef-infra/

#Ansible

#tools #devops #devops 2020 #tech tools #tool selection #tool comparison

Jones Brianna

Jones Brianna

1584681632

Pool Betting Software Development

Mobiweb Technologies is an expert Pool Betting Software Development Company providing services globally. Our experts can develop user-centric betting platforms that energize the bettors to bet online. Using latest techniques and features, Our team has specialized knowledge of creating pool betting software. If you have an idea to design pool betting software and are looking for a trustworthy partner then you can trust Team Mobiweb.

#Pool Betting Software #Pool Betting App Development #Pool Betting App Developers #Pool Betting Website Development #Pool Betting Software Providers