Bioinformatics Freelancing Training

About Course

NCBI
Sequence Format
UCSC
UniProt
PDB
ENSEMBL
InterPro
Phytozome
Pairwise Sequence Alignment & Analysis
Multiple Sequence Alignment & Analysis
Alignment Format
Sequence Analysis
Phylogenetic Analysis
Phylogenetic Tree Visualization & Analysis
Secondary Structure Prediction
Protein Analysis
Protein Family Database
Motif & Domain Analysis
3D Structure Prediction
3D Structure Visualization
3D Structure Evaluation
Molecular Docking
Docking Complex Evaluation
Gene Prediction
PPI Database
Genomic Tools
Molecular Dynamics Simulation
Molecular Dynamics Simulations: GROMACS
Vaccine Development
Introduction to Python
Iterable Objects
Control Flow
File Handling
Functions & Modules
Error Handling
Introduction to BioPython
Sequence Analysis in BioPython
Sequence Data Parsing
Sequence Data Extraction
Alignment Parsing and Analysis
BLAST Database Searching
Parsing BLAST results
Biological Data Retrieval
Parsing a PDB Structure file
Phylogenetic Analysis in BioPthon
R
Linux

Course Content

Bioinformatics Freelancing Training

In-Depth Introduction to Bioinformatics Freelancing

31:44
In-depth guide on FIVERR

13:51
In-depth guide on Upwork

14:44
What kind of services can you sell as a Bioinformatician?

09:24
What exactly do you need to learn to provide your services?

12:40
How to connect with clients and accept their projects?

14:19
Case Study 1: Mutagenesis of Proteins Using PyMol

09:53
Case Study 2: Scripting for biological analysis

08:11
Case Study 3: Functional Bioinformatics Analysis

01:08:16

Bioinformatics Databases

Introduction to National Center of Biotechnology Information (NCBI)

18:02
Sequence Analysis

17:59
Sequence Retrieval from NCBI

16:17
PubMed Central & ENTREZ

11:07
GenBank: Nucleotide Database on NCBI

06:50
FASTA vs GenBank

18:26
Gene Database: A Comprehensive Gene Database

30:21
NCBI Genomes & NCBI Assembly: Retrieval of Genomes

36:14
RefSeq Database: Retrieval of Single Reference Sequences

11:16
BLAST Database Searching

25:37
Introduction to Molecular Modeling Database

08:07
Database of Short Genetic Variations (dbSNP)

12:16
HomoloGene: Discovery of Gene and Protein Families

06:11
Taxonomy

09:57
Introduction to UCSC Genome Browser & SARS-CoV-2 Viral Genome

13:40
Retrieve an Entire Genome & Retrieval of SARS-CoV-2 Viral Genome

09:41
Retrieval of Genomic Data & Annotation of SARS-CoV2 Viral Genome

05:30
Table Browser & SARS-CoV-2 Viral Genome

12:16
Visualization of Genomic Data on the Genome Browser & SARS-CoV-2 Genome

10:51
UniProt BLAST – Database Searching

12:33
UniProt Peptide Search – Find Regions Within UniProt Database

03:15
Introduction to ENSEMBL

07:50
Retrieval of a Gene-Protein-Chromosomal Region

18:02
Genome Assembly Retrieval and Analysis

10:24
Gene Analysis & Annotation

34:40
Variation Analysis

24:37
ENSEMBL BLAST/BLAT

15:08
Regulation – Understand the Influence of Regulatory Elements on Genes

04:19
Comparative Genomics Analysis

05:35
Introduction to Phytozome

09:39
Interpret Plant Genome Records

09:07
Download an Entire Plant Genome & Proteome

26:41
Keyword or BLAST Search in a Plant Genome

15:58
Visualize a Plant Genome Using JBrowse

17:38
UniProt Align – Pairwise & Multiple Sequence Alignment and Annotation

03:48
UniRef And Retrieve Protein Clusters

11:36
UniParc And Find the Non-Redundant Entries

04:59
Genome Reference Consortium (GRC)

07:48
BioProject

06:40
BioSystems

04:16
BioSample

02:56
Sequence Read Archive (SRA)

07:15
Introduction to Gene Expression Omnibus Database

09:16
Gene Expression Omnibus – Platforms

05:42
Gene Expression Omnibus – Samples

04:16
Gene Expression Omnibus – Series

04:01
Gene Expression Omnibus – Datasets

04:45

Bioinformatics File Formats

FASTA (Sequence Format)

06:13
GenBank (Sequence Annotation Format)

07:08
FASTQ Format

18:02
Gene File Format/Gene Transfer Format

11:07
BED (Gene Structure Format)

04:27
SAM

09:07
BAM

09:07
Clustal Omega Alignment Format

05:32
MEGA (Alignment Format)

05:32
PHYLIP – Multiple Sequence Alignment Format

04:35
Stockholm Alignment Format

03:10

Protein Databases & Analysis

Introduction to UniProt

09:56
UniProtKB & Protein Analysis

39:30
UniProteome & Retreieval of an Entire Proteome

13:05
UniProt BLAST – Database Searching

12:33
ID Mapping & Making Analysis Easier

07:17
Introduction to Protein Data Bank (PDB)

06:45
Accurately Searching for a Protein Structure on PDB & Protein Analysis

13:56
Biological Annotation and Protein Features View & Analysis

08:18
Browsing PDB According to Annotation

06:52
Digging Out Categorized & Specific Protein Structures from PDB Archives

06:23
Alignment Between Two PDB Sequences & Structures

06:08
3D Structure Visualization on PDB

10:49
Mapping Genomic Position to Protein Sequence and 3D Structure

04:35
Genomic Discovery of Protein Structure Through Gene

04:07
PDB – Protein Symmetry

02:34
Introduction to InterPro

04:10
InterPro – Protein Family Classification and Analysis

14:35
InterPro – Protein & Protein Domain Analysis

09:29
HMMER – Hidden Markov Model Based Protein Profiles Database

13:16
SignalP: Prediction of Signal Peptides

07:57
TargetP: Prediction of Protein Localization

09:22
Pfam – Understand the Relation of a Protein to its Family and Clan

15:56
PROSITE – A Database of Protein Domain, Families and Functional Sites

13:46
ScanProsite – Scanning Protein for Important Protein Sites Against PROSITE Database

07:36
Marcoil – Predict Coiled Coil Domains in Proteins

04:06
SMART

06:45
PDB – Ligands

05:23

Sequence Alignment & Analysis

EMBOSS NEEDLE: Global Alignment of Sequences

20:02
Clustal Omega: Most Reliable Multiple Sequence Alignment Tool

19:18
EMBOSS Water

09:10
Jalview

13:42
T-Coffee: Iterative Multiple Sequence Alignment Tool

08:38
MUSCLE: Accurate Multiple Sequence Alignment Tool

21:08
MEGA – Multiple Sequence Alignment

04:23
MAFFT – Fastest Multiple Sequence Alignment Tool

08:22
Aln2Plot

02:31

Phylogenetic Analysis

Secondary Structure Prediction

3D Structure Prediction

3D Structure Visualization

3D Structure Evaluation

Molecular Docking

MOE: Protein Ligand Docking

09:23
MOE: Protein Protein Docking

11:39
SwissDock Protein Ligand Docking

19:16
Autodock Vina Protein Ligand Docking

15:49
MOE: Docking Library of Compounds

19:48
MOE: Structure Based Drug Designing

16:19
ClusPro Protein Protein Docking

21:44
Patchdock Protein Protein Docking

17:40
PEPFOLD 3 Peptide Structure Prediction

13:15
Zdock Protein Protein/Ligand docking

19:35
MDockPEP Protein Peptide Docking

10:06
Discovery Studio+

12:03

Docking Complex Evaluation

Gene Prediction

PPI Database

Genomics Tools

Molecular Dynamics Simulation

Getting Started With Molecular Dynamics Simulation – Pre-processing of Protein Structure and Removal of Unnecessary Structural Features

12:34
pdb2gmx – Construction of Topology File for Simulation

09:01
Defining a Solvant Box for Simulation

04:14
Solvation – Adding Water Molecules in Solvant Box

05:31
Generating Input Run File Replacement of Water Molecules With Ions

06:55
Genion – Replacement of Water Molecules With Ions

04:19
Energy Minimization – Relaxing and Fixing the Structure for Simulation

11:25
GRACE – Visualization and Analysis of Minimized Structure

04:12
Equibiliration of Protein Structure NVT ENSEMBLE Phase 1

08:38
Equibiliration of Protein Structure NPT ENSEMBLE Phase 2

08:10
mdrun – Executing Simulation Analysis

03:47

Python

Introduction to Python and it’s Installation

08:25
Why Python in Bioinformatics

09:16
Comments

05:43
Basic Input and output

15:38
Mathematical Operations

07:20
Strings

21:51
Dictionaries

10:57
Lists

28:48
Lists (pt 2) and Tuples

10:38
Sets

07:36
If-Else

09:19
For Loop and Calculation of Molecular Weight of Proteins

10:56
While Loop and Biological Data Analysis

09:37
Reading Files

13:45
CSV (A special kind of file in Bioinformatics)

08:42
Writing Files

07:18
Consolidate (merge) multiple DNA and Protein Sequences into one FASTA file

09:25
OS

31:47
Function

26:41
With

08:50
Error Handling

15:31

BioPython

Introduction to BioPython & Installation

10:19
Bio.Seq Seq Object Behaves Like a String

09:54
Bio.Seq Create a Seq Object

07:34
Bio.Seq Central Dogma in Play Through Python

08:41
Bio.Seq Unknown & Mutable Sequences

06:54
Bio.Alphabet Understanding the Alphabets of Biology

07:38
Bio.Alphabet IUPAC and Types of Sequence Representations

07:38
Bio.Alphabet Concatenation of Multiple Seq Records Using Generic Alphabets

09:47
SeqRecord Creating Seq Records

12:28
SeqRecords & FASTA

04:36
SeqRecords & GenBank

03:29
SeqRecord Formatting Records

03:06
SeqRecord Comparison & Reading Multiple FASTA Files from Directory

05:47
SeqIO Reading a Sequence File

10:32
SeqIO – Write Sequences and SeqRecords Into Files

11:43
SeqIO Extracting Annotations and Pattern-wise Sequence Data Extraction

10:35
AlignIO – Writing Alignments and Multiple Sequence Alignment Records

05:29
AlignIO – Conversion of Alignment Formats

04:02
AlignIO – Manipulating Alignments

02:57
AlignIO – ClustalW Python Wrapper – Align Multiple Sequences

07:47
AlignIO – Pairwise2 – Align Two Sequences

07:31
AlignIO – Information Mapping of Alignments

02:33
AlignIO – Format Alignments

03:36
AlignIO – Slicing Alignments

06:06
Bio.Blast – Querying NCBI BLAST Through Python

11:15
Draft LessonBio.Blast – Parsing BLAST Results

14:52
Bio.Entrez – Accessing ENTREZ Using Python

09:32
Bio Entrez Use Esummary To Get Summary Of Your Accessions

08:59
Bio.Entrez – Use EFetch to Download Complete Records

13:57
Bio.Entrez – Use EGQuery to Do Global Quries for Search Counts

07:24
Bio.Entrez – Use Elink To Search For Database Links Of Records

03:42
Bio.Entrez – Use ESearch to Search the Entrez Databases

08:20
Bio.Entrez – Use Espell To Get Correct Spellings For Your Search Terms

05:21
Bio.Entrez – Download GenBank and Entrez Records

14:17
Bio.Entrez – Taxonomy Database Searching

07:05
Bio.Entrez – Download PubMed Articles

08:28
Bio.PDB – Reading a PDB (3D Structure) File

11:59
Bio.Phylo – Calculating Distance Matrix Between Sequences For Phylogenetic Analysis

04:18
Bio.Phylo – Converting Phylogenetic Tree Data Formats

03:29
Bio.Phylo – Printing Out Phylogenetic Tree In Ascii

02:17
Bio.Phylo – Reading Phylogenetic Trees

06:29
Bio.Phylo – Visualization And Manipulation Of Phylogenetic Trees

09:36
Bio.motifs – Creating a WebLogo of Motifs

10:47
Bio.Phylo – Writing Out Phylogenetic Data

04:04
Bio.motifs – MEME Analysis

09:49

R

Introduction to R in Bioinformatics & R Installation

09:48
The R User Interface

06:23
Comments

04:17
Variable Declaration and Objects

05:24
Built-in Functions & ARGS

04:32
Sample & Replacement

09:09
Write Your Own Functions And Arguments

05:39
Scripts

07:36
Packages

04:00
Install Packages

05:25
Library & Initialize Packages

02:28
Getting Help with Help Packages

03:43
Atomic Vectors

02:43
Doubles

03:31
Integers

03:23
Characters

04:43
Logicals

02:27
Attributes and Names

04:46
Dim & Dimensions

05:46
Matrix & Matrices

04:43
Arrays

03:42
Class

03:13
Factors

06:41
Lists

06:42
Coercion

04:27
Data Frames

06:30
Loading Biological Data

07:56
Saving Biological Data

05:27
R Notation & Selecting Values from Biological Dataset

04:09
Negative Integers for subsetting Biological Dataset (DataFrame)

05:28
Positive Integers for subsetting Biological Dataset (DataFrame)

05:26
Zero Notation for subsetting Biological Datasets (DataFrames)

01:09
Blank Spaces For Biological Data Subsetting

03:21
Dollar Signs for Biological Dataset Subsetting

02:58
Modifying Values in Existing DataFrames/Datasets

07:06
NA Values in Biological Dataset

05:25
Figuring out NA Values in Biological Dataset

02:06
Logical Subsetting in Biological Datasets

09:46
If Else Statement

04:15
For Loops & Biological Data Binding

16:30
While Loops & Reading Multiple Biological Datasets

16:16
Introduction to ggplot2 for Biological Datasets

10:46
ggplot2: Key components

08:26
ggplot2: Human Mitochondrial Proteome & Aesthetics (Size, Shape, Color)

26:06
ggplot2: Facetting of Human Genome

22:25
ggplot2: Smooth Out the Biological Data

08:43
ggplot2: Boxplots for Human Mitochondrial Proteome

07:56
ggplot2 :Histograms for Human Mitochondrial Pattern Finding

06:02
ggplot2: Frequency Plots for Human Mitochondrial Information Frequency Mining

06:13
ggplot2: Bar Charts Human Mitochondrial Knowledge Mining

10:43
ggplot2 – Scaling and Limiting Data Visualization

03:53
ggplot2 – Changing Labels and Finalizing Visualization

08:42
ggtree – Phylogenetic Tree Visualization

05:41
ggplot2 – Saving the Visualizations in High Resolution

04:45

Linux

Introduction to Linux for Bioinformatics

22:32
PWD – Print Working Directory

01:26
CD – Changing Directories

05:03
MKDIR – Making Directories

08:13
MV – Moving Files, Directories and Data

05:11
RM – Deleting Files and Directories

01:24
Which & Whereis – Find Programs You Installed

03:43
LS – Listing Files and Directories on Linux

06:46
Find – Finding User Created Files

03:39
Piping and Redirection of Data

06:35
Cat – Visualization and Inspection of Text Data

03:56
Head – Reading Specified Number of Lines from Top

03:50
Tail- Reading Specified Number of Lines from Bottom

02:23
Touch – Modifying File Statistics and Creating Files

07:04
Stat – Statistics of File & Directories

02:43
Wget – Retrieval of Genome Assemblies

06:48
Curl – Retrieval of Bioinformatics Files

02:25
Vim – Create and Edit Text Files

05:59
Diff – Find Sequence Differences in Files

02:35
GZIP – Compress and Archive Files Efficiently

06:05
Tar – Create Archives of Genome Data

04:19
GUNZIP – Extract Compressed Content

02:14
Grep – Finding Uncharacterized Proteins in Human Genome

08:55
Cut – Subsetting Required Textual Data from Text Files

05:49
Sort – Sorting Data

04:23
Uniq – Finding Unique Data Items

10:33
WC – Statistics of the Data Within File

02:46
CP – Copying Files and Files Contents

03:43
Column – Proper Visualization of Delimited Datasets

04:38

R

Introduction to BioConductor

10:28
Installing Packages from BioConductor

04:12
Reading and Writing the FASTA File

06:58
Getting the Detail of a Sequence Composition

07:46
Pairwise Sequence Alignment

08:08
Multiple Sequence Alignment

09:47
Handling BLAST Results

03:54
Pattern Finding in a Sequence

05:51
Performing ID Conversions

05:45
The GO Annotation of Genes

04:33
The GO Enrichment of Genes

09:28
The KEGG Enrichment of Genes

07:16
Introduction to dplyr

15:38
Filter Rows with filter()

20:13
Select Columns with select()

28:30
Add New Variables with mutate()

21:19
Grouped Summaries with summerize()

18:30
Grouped Mutates (and Filters)

19:58
Introduction to tidyr

11:35
Data Spreading Function

13:51
Data Gathering Function

19:30
Data Separating & Pull

17:24
Missing Values

29:58

Introduction to Microarray Analysis & R

Quality Control & Normalization

Principle Component Analysis of Raw Expression Dataset

15:44
Box Plot Visualization of Raw Intensity Data to Interpret the Median Intensities of the Samples

03:11
ArrayQualityMetrics – Automated Quality Control for Microarray Datasets

05:38
Robust Multi-Array Summarization and Background Correction of the Raw MicroArray Data

03:47
Relative Log Expression Analysis and Visualization

08:57
Normalization of Raw Intesnities Values

04:36
Heatmap Visualization of the Normalized Gene Expression Values

11:52
Intensity-based Filtration of Low-Intensity Transcripts

06:19
Filtering out the Genes that are Above Threshold

06:02
Annotating the Probe IDs with Gene Symbols and Names

04:19
Removal of the Probe IDs that Match to Multiple Genes

04:04
Excluding Probe IDs with Multiple Mappings from the ExpressionSet

04:39

Differential Expression Analysis

LIMMA – Data Preparation for Linear Modelling

11:49
Factors Preparation

10:26
Analysis of Gene Expression Levels of a Single Gene Among Different Conditions

12:00
Applying t-test to Find if Genes are Differentially Expression

06:51
LIMMA – Applying Linear Model on a Single Gene Expression Data

05:34
LIMMA – Applying Linear Model for Differential Gene Expression Analysis

11:38
Extraction of Differentially Expressed Genes from the Fitted Linear Model

03:35
Setting a Threshold for Differentially Expressed Genes

04:17
Volcano Plot – Visualization of the Genes that are Differentially Expressed

04:36
Downstream Functional Enrichment Analysis Using enrichR – Gene Ontology & KEGG Pathways Analysis

08:44

Target Identification

Immunoinformatics Approach for Epitope Prediction

Computational Construction of the Vaccine

Molecular Dynamics and Immune Simulation

Supplementary 1

Supplementary 2

Supplementary 3

Introduction to NGS, RNA-Seq Pipeline & GALAXY

Practical RNA-Seq Differential Gene Expression Analysis

Evaluation

Add this certificate to your resume to demonstrate your skills & increase your chances of getting noticed.

Student Ratings & Reviews

No Review Yet

About Course

What Will You Learn?

Course Content

Bioinformatics Freelancing Training

In-Depth Introduction to Bioinformatics Freelancing

In-depth guide on FIVERR

In-depth guide on Upwork

What kind of services can you sell as a Bioinformatician?

What exactly do you need to learn to provide your services?

How to connect with clients and accept their projects?

Case Study 1: Mutagenesis of Proteins Using PyMol

Case Study 2: Scripting for biological analysis

Case Study 3: Functional Bioinformatics Analysis

Bioinformatics Databases

Introduction to National Center of Biotechnology Information (NCBI)

Sequence Analysis

Sequence Retrieval from NCBI

PubMed Central & ENTREZ

GenBank: Nucleotide Database on NCBI

FASTA vs GenBank

Gene Database: A Comprehensive Gene Database

NCBI Genomes & NCBI Assembly: Retrieval of Genomes

RefSeq Database: Retrieval of Single Reference Sequences

BLAST Database Searching

Introduction to Molecular Modeling Database

Database of Short Genetic Variations (dbSNP)

HomoloGene: Discovery of Gene and Protein Families

Taxonomy

Introduction to UCSC Genome Browser & SARS-CoV-2 Viral Genome

Retrieve an Entire Genome & Retrieval of SARS-CoV-2 Viral Genome

Retrieval of Genomic Data & Annotation of SARS-CoV2 Viral Genome

Table Browser & SARS-CoV-2 Viral Genome

Visualization of Genomic Data on the Genome Browser & SARS-CoV-2 Genome

UniProt BLAST – Database Searching

UniProt Peptide Search – Find Regions Within UniProt Database

Introduction to ENSEMBL

Retrieval of a Gene-Protein-Chromosomal Region

Genome Assembly Retrieval and Analysis

Gene Analysis & Annotation

Variation Analysis

ENSEMBL BLAST/BLAT

Regulation – Understand the Influence of Regulatory Elements on Genes

Comparative Genomics Analysis

Introduction to Phytozome

Interpret Plant Genome Records

Download an Entire Plant Genome & Proteome

Keyword or BLAST Search in a Plant Genome

Visualize a Plant Genome Using JBrowse

UniProt Align – Pairwise & Multiple Sequence Alignment and Annotation

UniRef And Retrieve Protein Clusters

UniParc And Find the Non-Redundant Entries

Genome Reference Consortium (GRC)

BioProject

BioSystems

BioSample

Sequence Read Archive (SRA)

Introduction to Gene Expression Omnibus Database

Gene Expression Omnibus – Platforms

Gene Expression Omnibus – Samples

Gene Expression Omnibus – Series

Gene Expression Omnibus – Datasets

Bioinformatics File Formats

FASTA (Sequence Format)

GenBank (Sequence Annotation Format)

FASTQ Format

Gene File Format/Gene Transfer Format

BED (Gene Structure Format)

SAM

BAM

Clustal Omega Alignment Format

MEGA (Alignment Format)

PHYLIP – Multiple Sequence Alignment Format

Stockholm Alignment Format

Protein Databases & Analysis

Introduction to UniProt

UniProtKB & Protein Analysis

UniProteome & Retreieval of an Entire Proteome

UniProt BLAST – Database Searching

ID Mapping & Making Analysis Easier

Introduction to Protein Data Bank (PDB)