De bruijn graphs
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it will help to understood about de bruijn graph clearly also helps to understand K-MER concept in genome analysis.
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De bruijn graphs
De Bruijn graphs are directed graphs used to represent overlaps between sequences of symbols. They are constructed by splitting a DNA sequence into k-mers (subsequences of length k), creating nodes for each k-mer, and connecting nodes with edges where the k-mers overlap by k-1 nucleotides. De Bruijn graphs are commonly used for genome assembly from next-generation sequencing data by reconstructing the original sequence from the k-mers. They allow mapping short reads onto a reference genome despite the reads being shorter than the repeats within the genome.
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New generation sequencing equipments
This document summarizes three main next generation sequencing technologies: Roche/454FLX pyrosequencing, Illumina/Solexa sequencing by synthesis, and Applied Biosystems SOLiD sequencing by ligation. Pyrosequencing works by detecting pyrophosphate released during DNA polymerization, producing light signals to determine the sequence. Roche/454FLX amplifies DNA fragments on beads in emulsions and sequences in picotiter plates. Illumina attaches DNA fragments to a flow cell for bridge amplification and sequencing by synthesis. Applied Biosystems SOLiD performs sequencing by ligation, determining sequences through sequential ligation of oligos.
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De bruijn graphs
De Bruijn graphs are directed graphs used to represent overlaps between sequences of symbols. They are constructed by splitting a DNA sequence into k-mers (subsequences of length k), creating nodes for each k-mer, and connecting nodes with edges where the k-mers overlap by k-1 nucleotides. De Bruijn graphs are commonly used for genome assembly from next-generation sequencing data by reconstructing the original sequence from the k-mers. They allow mapping short reads onto a reference genome despite the reads being shorter than the repeats within the genome.
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First part of the presentation slides of 'RNA-seq for DE analysis.'. See http://www.bits.vib.be for more information.
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1) A brief history of sequencing technologies and their improvements over time, from Sanger sequencing to newer technologies producing longer reads.
2) Key steps in a sequencing project including read processing, filtering, and corrections before assembly into contigs and scaffolds using appropriate software.
3) Factors to consider for experimental design and assembly optimization such as sequencing depth, library types, and software choices depending on the genome and data characteristics.
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- Making sense of the large and complex RNA-Seq data depends on the scientific question, such as finding transcribed SNPs for allele-specific expression or novel transcripts in cancer samples.
- Common applications of RNA-Seq include abundance estimation, alternative splicing detection, RNA editing discovery, and finding novel transcripts and isoforms.
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- Genomics involves mapping and sequencing genomes to understand genes and how they function. It uses techniques from genetics and molecular biology.
- The human genome contains 23 chromosome pairs and around 24,000 genes. Genomics aims to sequence whole genomes and analyze gene function.
- Early developments included identifying DNA's structure in 1953 and sequencing the first genome in the 1970s. The Human Genome Project aimed to map the entire human genome between 1990-2003.
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2) Key steps in a sequencing project including read processing, filtering, and corrections before assembly into contigs and scaffolds using appropriate software.
3) Factors to consider for experimental design and assembly optimization such as sequencing depth, library types, and software choices depending on the genome and data characteristics.
RNA-seq: A High-resolution View of the Transcriptome
The molecular microscopes that we use to examine human biology have advanced significantly with the advent of next generation sequencing. RNA-seq is one application of this technology that leads to a very high-resolution view of the transcriptome. With these new technologies come increased data analysis and data handling burdens as well as the promise of new discovery. These slides present a high-level overview of the RNA-seq technology with a focus on the analysis approaches, quality control challenges, and experimental design.
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The document discusses RNA-Seq data analysis. Some key points:
- RNA-Seq involves sequencing steady-state RNA in a sample without prior knowledge of the organism. It can uncover novel transcripts and isoforms.
- Making sense of the large and complex RNA-Seq data depends on the scientific question, such as finding transcribed SNPs for allele-specific expression or novel transcripts in cancer samples.
- Common applications of RNA-Seq include abundance estimation, alternative splicing detection, RNA editing discovery, and finding novel transcripts and isoforms.
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* High throughput sequencing basics and choices
* Cost estimation
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* Assigning reads to genes and counting
* Analysis of differentially expressed genes
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Sequence Assembly
This document discusses DNA sequencing and sequence assembly. It defines sequencing as determining the order of nucleotides in DNA, and sequence assembly as aligning and merging DNA fragments to reconstruct the original sequence. It describes the shotgun sequencing method using Sanger sequencing that randomly fragments DNA, sequences the fragments, and assembles the sequence by finding overlaps between fragments. It provides an example of fragmenting and assembling a DNA sequence. It discusses using long reads for sequencing, which have higher error rates but allow assembly into longer contigs compared to short read sequencing.
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https://medium.com/@tspann
https://www.datainmotion.dev/
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一比一原版(UMN文凭证书)明尼苏达大学毕业证如何办理
毕业原版【微信:176555708】【(UMN毕业证书)明尼苏达大学毕业证】【微信:176555708】成绩单、外壳、offer、留信学历认证（永久存档真实可查）采用学校原版纸张、特殊工艺完全按照原版一比一制作（包括：隐形水印，阴影底纹，钢印LOGO烫金烫银，LOGO烫金烫银复合重叠，文字图案浮雕，激光镭射，紫外荧光，温感，复印防伪）行业标杆！精益求精，诚心合作，真诚制作！多年品质 ,按需精细制作，24小时接单,全套进口原装设备，十五年致力于帮助留学生解决难题，业务范围有加拿大、英国、澳洲、韩国、美国、新加坡，新西兰等学历材料，包您满意。
【我们承诺采用的是学校原版纸张（纸质、底色、纹路），我们拥有全套进口原装设备，特殊工艺都是采用不同机器制作，仿真度基本可以达到100%，所有工艺效果都可提前给客户展示，不满意可以根据客户要求进行调整，直到满意为止！】
【业务选择办理准则】
一、工作未确定，回国需先给父母、亲戚朋友看下文凭的情况，办理一份就读学校的毕业证【微信176555708】文凭即可
二、回国进私企、外企、自己做生意的情况，这些单位是不查询毕业证真伪的，而且国内没有渠道去查询国外文凭的真假，也不需要提供真实教育部认证。鉴于此，办理一份毕业证【微信176555708】即可
三、进国企，银行，事业单位，考公务员等等，这些单位是必需要提供真实教育部认证的，办理教育部认证所需资料众多且烦琐，所有材料您都必须提供原件，我们凭借丰富的经验，快捷的绿色通道帮您快速整合材料，让您少走弯路。
留信网认证的作用:
1:该专业认证可证明留学生真实身份
2:同时对留学生所学专业登记给予评定
3:国家专业人才认证中心颁发入库证书
4:这个认证书并且可以归档倒地方
5:凡事获得留信网入网的信息将会逐步更新到个人身份内，将在公安局网内查询个人身份证信息后，同步读取人才网入库信息
6:个人职称评审加20分
7:个人信誉贷款加10分
8:在国家人才网主办的国家网络招聘大会中纳入资料，供国家高端企业选择人才
留信网服务项目：
1、留学生专业人才库服务（留信分析）
2、国（境）学习人员提供就业推荐信服务
3、留学人员区块链存储服务
→ 【关于价格问题（保证一手价格）】
我们所定的价格是非常合理的，而且我们现在做得单子大多数都是代理和回头客户介绍的所以一般现在有新的单子 我给客户的都是第一手的代理价格，因为我想坦诚对待大家 不想跟大家在价格方面浪费时间
对于老客户或者被老客户介绍过来的朋友，我们都会适当给一些优惠。
选择实体注册公司办理，更放心，更安全！我们的承诺：客户在留信官方认证查询网站查询到认证通过结果后付款，不成功不收费！
一比一原版(UO毕业证)渥太华大学毕业证如何办理
原件一模一样【微信：95270640】【渥太华大学毕业证UO学位证成绩单】【微信：95270640】（留信学历认证永久存档查询）采用学校原版纸张、特殊工艺完全按照原版一比一制作（包括：隐形水印，阴影底纹，钢印LOGO烫金烫银，LOGO烫金烫银复合重叠，文字图案浮雕，激光镭射，紫外荧光，温感，复印防伪）行业标杆！精益求精，诚心合作，真诚制作！多年品质 ,按需精细制作，24小时接单,全套进口原装设备，十五年致力于帮助留学生解决难题，业务范围有加拿大、英国、澳洲、韩国、美国、新加坡，新西兰等学历材料，包您满意。
【业务选择办理准则】
一、工作未确定，回国需先给父母、亲戚朋友看下文凭的情况，办理一份就读学校的毕业证【微信：95270640】文凭即可
二、回国进私企、外企、自己做生意的情况，这些单位是不查询毕业证真伪的，而且国内没有渠道去查询国外文凭的真假，也不需要提供真实教育部认证。鉴于此，办理一份毕业证【微信：95270640】即可
三、进国企，银行，事业单位，考公务员等等，这些单位是必需要提供真实教育部认证的，办理教育部认证所需资料众多且烦琐，所有材料您都必须提供原件，我们凭借丰富的经验，快捷的绿色通道帮您快速整合材料，让您少走弯路。
留信网认证的作用:
1:该专业认证可证明留学生真实身份【微信：95270640】
2:同时对留学生所学专业登记给予评定
3:国家专业人才认证中心颁发入库证书
4:这个认证书并且可以归档倒地方
5:凡事获得留信网入网的信息将会逐步更新到个人身份内，将在公安局网内查询个人身份证信息后，同步读取人才网入库信息
6:个人职称评审加20分
7:个人信誉贷款加10分
8:在国家人才网主办的国家网络招聘大会中纳入资料，供国家高端企业选择人才
→ 【关于价格问题（保证一手价格）
我们所定的价格是非常合理的，而且我们现在做得单子大多数都是代理和回头客户介绍的所以一般现在有新的单子 我给客户的都是第一手的代理价格，因为我想坦诚对待大家 不想跟大家在价格方面浪费时间
对于老客户或者被老客户介绍过来的朋友，我们都会适当给一些优惠。
选择实体注册公司办理，更放心，更安全！我们的承诺：可来公司面谈，可签订合同，会陪同客户一起到教育部认证窗口递交认证材料，客户在教育部官方认证查询网站查询到认证通过结果后付款，不成功不收费！
办理渥太华大学毕业证毕业证offerUO学位证【微信：95270640 】外观非常精致，由特殊纸质材料制成，上面印有校徽、校名、毕业生姓名、专业等信息。
办理渥太华大学毕业证UO学位证毕业证offer【微信：95270640 】格式相对统一，各专业都有相应的模板。通常包括以下部分：
校徽：象征着学校的荣誉和传承。
校名:学校英文全称
授予学位：本部分将注明获得的具体学位名称。
毕业生姓名：这是最重要的信息之一，标志着该证书是由特定人员获得的。
颁发日期：这是毕业正式生效的时间，也代表着毕业生学业的结束。
其他信息：根据不同的专业和学位，可能会有一些特定的信息或章节。
办理渥太华大学毕业证毕业证offerUO学位证【微信：95270640 】价值很高，需要妥善保管。一般来说，应放置在安全、干燥、防潮的地方，避免长时间暴露在阳光下。如需使用，最好使用复印件而不是原件，以免丢失。
综上所述，办理渥太华大学毕业证毕业证offerUO学位证【微信：95270640 】是证明身份和学历的高价值文件。外观简单庄重，格式统一，包括重要的个人信息和发布日期。对持有人来说，妥善保管是非常重要的。
Build applications with generative AI on Google Cloud
We will explore Vertex AI - Model Garden powered experiences, we are going to learn more about the integration of these generative AI APIs. We are going to see in action what the Gemini family of generative models are for developers to build and deploy AI-driven applications. Vertex AI includes a suite of foundation models, these are referred to as the PaLM and Gemini family of generative ai models, and they come in different versions. We are going to cover how to use via API to: - execute prompts in text and chat - cover multimodal use cases with image prompts. - finetune and distill to improve knowledge domains - run function calls with foundation models to optimize them for specific tasks. At the end of the session, developers will understand how to innovate with generative AI and develop apps using the generative ai industry trends.
4th Modern Marketing Reckoner by MMA Global India & Group M: 60+ experts on W...
The Modern Marketing Reckoner (MMR) is a comprehensive resource packed with POVs from 60+ industry leaders on how AI is transforming the 4 key pillars of marketing – product, place, price and promotions.
一比一原版(UCSB文凭证书)圣芭芭拉分校毕业证如何办理
毕业原版【微信:176555708】【(UCSB毕业证书)圣芭芭拉分校毕业证】【微信:176555708】成绩单、外壳、offer、留信学历认证（永久存档真实可查）采用学校原版纸张、特殊工艺完全按照原版一比一制作（包括：隐形水印，阴影底纹，钢印LOGO烫金烫银，LOGO烫金烫银复合重叠，文字图案浮雕，激光镭射，紫外荧光，温感，复印防伪）行业标杆！精益求精，诚心合作，真诚制作！多年品质 ,按需精细制作，24小时接单,全套进口原装设备，十五年致力于帮助留学生解决难题，业务范围有加拿大、英国、澳洲、韩国、美国、新加坡，新西兰等学历材料，包您满意。
【我们承诺采用的是学校原版纸张（纸质、底色、纹路），我们拥有全套进口原装设备，特殊工艺都是采用不同机器制作，仿真度基本可以达到100%，所有工艺效果都可提前给客户展示，不满意可以根据客户要求进行调整，直到满意为止！】
【业务选择办理准则】
一、工作未确定，回国需先给父母、亲戚朋友看下文凭的情况，办理一份就读学校的毕业证【微信176555708】文凭即可
二、回国进私企、外企、自己做生意的情况，这些单位是不查询毕业证真伪的，而且国内没有渠道去查询国外文凭的真假，也不需要提供真实教育部认证。鉴于此，办理一份毕业证【微信176555708】即可
三、进国企，银行，事业单位，考公务员等等，这些单位是必需要提供真实教育部认证的，办理教育部认证所需资料众多且烦琐，所有材料您都必须提供原件，我们凭借丰富的经验，快捷的绿色通道帮您快速整合材料，让您少走弯路。
留信网认证的作用:
1:该专业认证可证明留学生真实身份
2:同时对留学生所学专业登记给予评定
3:国家专业人才认证中心颁发入库证书
4:这个认证书并且可以归档倒地方
5:凡事获得留信网入网的信息将会逐步更新到个人身份内，将在公安局网内查询个人身份证信息后，同步读取人才网入库信息
6:个人职称评审加20分
7:个人信誉贷款加10分
8:在国家人才网主办的国家网络招聘大会中纳入资料，供国家高端企业选择人才
留信网服务项目：
1、留学生专业人才库服务（留信分析）
2、国（境）学习人员提供就业推荐信服务
3、留学人员区块链存储服务
→ 【关于价格问题（保证一手价格）】
我们所定的价格是非常合理的，而且我们现在做得单子大多数都是代理和回头客户介绍的所以一般现在有新的单子 我给客户的都是第一手的代理价格，因为我想坦诚对待大家 不想跟大家在价格方面浪费时间
对于老客户或者被老客户介绍过来的朋友，我们都会适当给一些优惠。
选择实体注册公司办理，更放心，更安全！我们的承诺：客户在留信官方认证查询网站查询到认证通过结果后付款，不成功不收费！
Predictably Improve Your B2B Tech Company's Performance by Leveraging Data
Harness the power of AI-backed reports, benchmarking and data analysis to predict trends and detect anomalies in your marketing efforts.
Peter Caputa, CEO at Databox, reveals how you can discover the strategies and tools to increase your growth rate (and margins!).
From metrics to track to data habits to pick up, enhance your reporting for powerful insights to improve your B2B tech company's marketing.
- - -
This is the webinar recording from the June 2024 HubSpot User Group (HUG) for B2B Technology USA.
Watch the video recording at https://youtu.be/5vjwGfPN9lw
Sign up for future HUG events at https://events.hubspot.com/b2b-technology-usa/
原版制作(unimelb毕业证书)墨尔本大学毕业证Offer一模一样
学校原件一模一样【微信：741003700 】《(unimelb毕业证书)墨尔本大学毕业证》【微信：741003700 】学位证，留信认证（真实可查，永久存档）原件一模一样纸张工艺/offer、雅思、外壳等材料/诚信可靠,可直接看成品样本，帮您解决无法毕业带来的各种难题！外壳，原版制作，诚信可靠，可直接看成品样本。行业标杆！精益求精，诚心合作，真诚制作！多年品质 ,按需精细制作，24小时接单,全套进口原装设备。十五年致力于帮助留学生解决难题，包您满意。
本公司拥有海外各大学样板无数，能完美还原。
1:1完美还原海外各大学毕业材料上的工艺：水印，阴影底纹，钢印LOGO烫金烫银，LOGO烫金烫银复合重叠。文字图案浮雕、激光镭射、紫外荧光、温感、复印防伪等防伪工艺。材料咨询办理、认证咨询办理请加学历顾问Q/微741003700
【主营项目】
一.毕业证【q微741003700】成绩单、使馆认证、教育部认证、雅思托福成绩单、学生卡等！
二.真实使馆公证(即留学回国人员证明,不成功不收费)
三.真实教育部学历学位认证（教育部存档！教育部留服网站永久可查）
四.办理各国各大学文凭(一对一专业服务,可全程监控跟踪进度)
如果您处于以下几种情况：
◇在校期间，因各种原因未能顺利毕业……拿不到官方毕业证【q/微741003700】
◇面对父母的压力，希望尽快拿到；
◇不清楚认证流程以及材料该如何准备；
◇回国时间很长，忘记办理；
◇回国马上就要找工作，办给用人单位看；
◇企事业单位必须要求办理的
◇需要报考公务员、购买免税车、落转户口
◇申请留学生创业基金
留信网认证的作用:
1:该专业认证可证明留学生真实身份
2:同时对留学生所学专业登记给予评定
3:国家专业人才认证中心颁发入库证书
4:这个认证书并且可以归档倒地方
5:凡事获得留信网入网的信息将会逐步更新到个人身份内，将在公安局网内查询个人身份证信息后，同步读取人才网入库信息
6:个人职称评审加20分
7:个人信誉贷款加10分
8:在国家人才网主办的国家网络招聘大会中纳入资料，供国家高端企业选择人才
一比一原版(GWU,GW文凭证书)乔治·华盛顿大学毕业证如何办理
毕业原版【微信:176555708】【(GWU,GW毕业证书)乔治·华盛顿大学毕业证】【微信:176555708】成绩单、外壳、offer、留信学历认证（永久存档真实可查）采用学校原版纸张、特殊工艺完全按照原版一比一制作（包括：隐形水印，阴影底纹，钢印LOGO烫金烫银，LOGO烫金烫银复合重叠，文字图案浮雕，激光镭射，紫外荧光，温感，复印防伪）行业标杆！精益求精，诚心合作，真诚制作！多年品质 ,按需精细制作，24小时接单,全套进口原装设备，十五年致力于帮助留学生解决难题，业务范围有加拿大、英国、澳洲、韩国、美国、新加坡，新西兰等学历材料，包您满意。
【我们承诺采用的是学校原版纸张（纸质、底色、纹路），我们拥有全套进口原装设备，特殊工艺都是采用不同机器制作，仿真度基本可以达到100%，所有工艺效果都可提前给客户展示，不满意可以根据客户要求进行调整，直到满意为止！】
【业务选择办理准则】
一、工作未确定，回国需先给父母、亲戚朋友看下文凭的情况，办理一份就读学校的毕业证【微信176555708】文凭即可
二、回国进私企、外企、自己做生意的情况，这些单位是不查询毕业证真伪的，而且国内没有渠道去查询国外文凭的真假，也不需要提供真实教育部认证。鉴于此，办理一份毕业证【微信176555708】即可
三、进国企，银行，事业单位，考公务员等等，这些单位是必需要提供真实教育部认证的，办理教育部认证所需资料众多且烦琐，所有材料您都必须提供原件，我们凭借丰富的经验，快捷的绿色通道帮您快速整合材料，让您少走弯路。
留信网认证的作用:
1:该专业认证可证明留学生真实身份
2:同时对留学生所学专业登记给予评定
3:国家专业人才认证中心颁发入库证书
4:这个认证书并且可以归档倒地方
5:凡事获得留信网入网的信息将会逐步更新到个人身份内，将在公安局网内查询个人身份证信息后，同步读取人才网入库信息
6:个人职称评审加20分
7:个人信誉贷款加10分
8:在国家人才网主办的国家网络招聘大会中纳入资料，供国家高端企业选择人才
留信网服务项目：
1、留学生专业人才库服务（留信分析）
2、国（境）学习人员提供就业推荐信服务
3、留学人员区块链存储服务
→ 【关于价格问题（保证一手价格）】
我们所定的价格是非常合理的，而且我们现在做得单子大多数都是代理和回头客户介绍的所以一般现在有新的单子 我给客户的都是第一手的代理价格，因为我想坦诚对待大家 不想跟大家在价格方面浪费时间
对于老客户或者被老客户介绍过来的朋友，我们都会适当给一些优惠。
选择实体注册公司办理，更放心，更安全！我们的承诺：客户在留信官方认证查询网站查询到认证通过结果后付款，不成功不收费！
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De bruijn graphs
- 2. CURIOUS QUESTIONS 1. What is the use ...? 2. Why to use …? 3. How to use …? 4. Where to use …?
- 3. HISTORY - The solution came in 1735, when the great mathematician Leonhard Euler. - Dutch mathematician Nicolaas de Bruijn(GIVES CYCLIC CONCEPT WITH LENTH “K”) DOI: 10.1038/nbt.2023 · Source: PubMed
- 4. WHY TO LERN ..? • NGS sequences use various software packages, such as Velvet, ABySS, Trinity, Oases, etc • To Reconstruct genomes from NGS libraries • •Creates unique pattern
- 5. HOW TO APPLY…? 1. Select the sequence(read) 2. k-mers are simply length k (read length) subsequences 3. to choose a k-mer size(3) 4. split the original sequence into its k-mer components 4. Directionality: whose last k-1 nucleotides are overlapping, to the k-mer, whose first k-1 nucleotides are overlapping.
- 6. HOW TO APPLY…? 5. Creating nodes 6. Highlight similar nodes closer 7. Glue the similar nodes
- 7. 8. Gluing identically vertices and labeling them HOW TO APPLY…?
- 8. HOW TO APPLY…? 9. Use whole sequence of first edge 10. The Only Use the last alphabets from the intermediate edges. 10. Build the genome
- 9. • Converting NGS sequence library to genome assembly • Eulerian walk (from de bruijn to reads) • RNAseq. Where to use …?
- 10. Drawbacks • De Bruijn graphs do not preserve positional information. • Longer the read size, more one has to lose. • Removing of Tips & Bubbles • k-mer size should be depends upon the read length
- 11. Overlap graph Vs de brujin graph AAABBBBA
- 12. MASSIVE DE BRUJIN GRAPH ERRORS:- 1) Sequencing error:- -creates tips and unnecessorily small nucliotides sequences TIP
- 13. • 2) POLYPLOIDY - this is not the error This is the real Scenario 3)REPEATS:- Eg.- ATATATATATATA MASSIVE DE BRUJIN GRAPH Bubble
- 14. REFERENCES 1) How to apply de Bruijn graphs to genome assembly :- DOI: 10.1038/nbt.2023 · Source: PubMed 2) Overlap graphs and de Bruijn graphs: https://doi.org/10.1007/s40484-019-0181-x 3). HOMOLOG.US :- https://homolog.us/Tutorials/book4/p1.1.ht ml 4) COURSERA :- https://www.coursera.org/