Register training material
15 materials found

Authors: allegra.via Via  or Dayane Araujo 


Discovering scientific evidence using Europe PMC SciLite annotation

For readers of life sciences journal articles, annotations make it easier to scan an article and get a quick overview, find key concepts, and discover evidence, such as gene disease associations or molecular interactions. This webinar will demonstrate how to use the power of text mining to find...

Keywords: Biomedical Literature, Annotations, Literature search, SciLite, Protein structure viewer, Chemical viewer

Resource type: Life Sciences Literature Database

Finding the data behind research publications with Europe PMC

This webinar will explain how to use Europe PMC to find relevant articles in your research field and locate the linked data containing facts and evidence to support your hypothesis.

Europe PMC is an open biomedical literature database including PubMed indexed articles, preprints,...

Keywords: Biomedical Literature, Data links, databases, External links

Resource type: Life Sciences Literature Database

Using Europe PMC for effective literature research

This webinar will explain how to find and access relevant scientific literature and show how you can follow the latest developments in your scientific field. It will cover searches by topic and author, searches for associated research data, as well as advanced options for building complex...

Keywords: Literature search, peer reviewed articles, Europe PMC, Preprints, Data links, Annotations, Europe PMC, ORCID

Resource type: Life Science Literature Database, Life Sciences Literature Database

Searching and browsing scientific publications with the new Europe PMC

Literature search is an essential and routine task in scientific research. Following the release of the new Europe PMC website, this webinar will show you the new full-text searching and browsing features built to optimise the literature research. Learn how to find the most recent, most relevant...

Keywords: Literature search, Data links, preprints

Resource type: Life Sciences Literature Database

How to Share Text Mining Results in Biology

Overview

Though text mining becomes more widespread in biology, an average researcher can rarely use it to their advantage. In this webinar, Europe PMC presents a tool to easily share annotated biological entities and relations with the research community. Europe PMC Annotation Submission...

Keywords: Europe PMC, Text mining, Literature search

Resource type: Webinar

Europe PMC, programmatically

Europe PMC is an open repository, providing access to worldwide biomedical literature, including articles, books, patents, and clinical guidelines. More than 32 million abstracts (27 million from PubMed) and 4 million full-text articles can be freely accessed through Europe PMC in a single...

Keywords: Literature search, Programmatic Access, Europe PMC, REST API, Biomedical Literature

Resource type: Webinar

Introduction to Biopython

This is a module from the "Python for Biologists" course. The module presents an introduction to Biopython. It shows how to deal with sequences and sequence records, how to download records from NCBI databases, how to run Blast and how to parse XML Blast outputs.

Keywords: Bioinformatics, Biopython, Programming, Python, Python biologists

Using R with Python

This is a module from the "Python for Biologists" course. It describes the Python module interfacing the R package for statistics. The module shows how to calculate mean, standard deviation, z-score and p-value of a set of numbers, and how to generate plots. Input files for the scripts presented...

Keywords: Programming, Python, Python biologists

Searching data using Python

This is a module from the "Python for Biologists" course. It describes how to use Python dictionary and set data structures to search your data. In particular, how to use a dictionary to represent the genetic code table and use it to translate a nucleotide sequence into a protein sequence, and...

Keywords: Programming, Python, Python biologists

Pattern Matching

This is a module from the "Python for Biologists" course. It teaches how to do pattern matching in Python, i.e. how to find a substring (or a set of substrings) in a string. To this aim, it introduces the regular expression syntax, and the tools needed to search regular expressions in biological...

Keywords: Pattern matching, Programming, Python, Python biologists

Writing functions in Python programming

This is a module from the "Python for Biologists" course. It deals with functions and how to write and use them. It also introduces namespaces and the tuple data structure. The module contains several exercises and suggested solutions. The text of exercises is also provided in a separate file. 

Scientific topics: Bioinformatics

Keywords: Programming, Python, Python biologists

Python Programs

This is a module from the "Python for Biologists" course. It deals with Python programs, how to write and run them, and how to provide input and generate output. The module also contains exercises and suggested solutions. 

Keywords: Programming, Python, Python biologists

Linear Motifs and Phosphorylation Sites

This is a lecture on linear motifs and phophorylation sites (P-sites). Some materials from other lectures are reused.
The lecture is basically about computational approaches to encode, predict, analyse, and use functional motifs and P-sites.
Here you can find:

    A definition of linear motifs and...

Keywords: Bioinformatics

Parsing data records using Python programming

This is a module from the "Python for Biologists" course. One typical problem in bioinformatics is parsing data files. This module explains how to parse FASTA files and GenBank records. It also introduces the if/elif/else construct to make choice in programming and the list  data structure. The...

Keywords: Bioinformatics, Programming, Python, Python biologists, Record parsing

Introduction to Unix

Introductory lecture to the Unix/Linux command-line

    Description of the computer shell and the command-line interface

    Differences between graphical and command-line interfaces

    The most commond Unix/Linux commands are provided

 
 

Keywords: Bioinformatics, Programming, Unixlinux