Bioinformatics Education - Summer School - An Introduction to Bioinformatics Algorithms (July 25-28) - Q&A

 At 2015-07-15 02:06:51 AM - 

Within the last 10 years, with the new development of Genome Sequencing methods, biotechnology has been in its revolution: many diseases has been detected and cured using the information from patients’ DNA; many new cells and their functions have been discovered based on single cell sequencing; many efficients drugs/vaccines been designed using the genomic information of viruses and human.

Computer algorithms, unarguably, play crucial roles in this development: Google, Microsoft, IBM, Intel, HP, Oracle, Wolfram, Illumina, Samsung… are now rushing into this field.

Students taking this course will learn the most advanced algorithms and their applications in the frontier of Bioinformatics research, will be able to work with real human genomic data and if exceptional, will involve in research collaborations with leading genomic institutions and will be mentored by world-class scientists.

Prerequisite:

  Basic knowledge in Algorithms and Programming.
  Practice your coding skills & have a feeling of bioinformatics at: rosalind.info/problems/list-view (optional)
  No knowledge in Biology is required.

If you have any question of running this tool or any suggestion please feel free to ask in this channel. 
 1 |   0 |   public

Etool support - Genomic Medicine 2015 - From 20 - 23 July 2015, HoChiMinh City, Vietnam

 At 2015-02-27 03:17:45 AM - 

General questions about the conference:
Conference chair: Ly Le
 Mobile: +84906578836
 Address: School of Biotechnology, International University, Vietnam National University.
 Email: ly.le@hcmiu.edu.vn

Question about the conference program and proceedings:
Conference co- chair: Son Pham
 Mobile: +18584364073
 Address: Department of computer science and engineering - University of California San Diego.
 Email: spham@salk.edu

Question about website and submission:
Admin: Hoa Pham
 Mobile: +841226119992
 Address: Department of computer science and engineering, Etool.Me Group.
 Email: thaihoabo@gmail.com

If you have any question, please write the below !!!
 2 |   0 |   public

Bioinformatics Education - Bioinformatics Algorithms: An Active Learning Approach

 At 2014-07-22 06:03:58 AM - 

The lecture videos for Bioinformatics Algorithms
 4 |   7 |   public

Bioinformatics Education - C/C++ Village

 At 2014-03-07 11:28:33 PM - 

If you are completely new to programming, try these initial problems to learn a few basics about the C/C++ programming language. You'll get familiar with the operations needed to start solving bioinformatics challenges in the Stronghold.
 1 |   0 |   public

Comparative Genomics - Bordetella Project

 At 2013-11-05 10:38:32 AM - 

Bordetella Genome Comparison Project.

In this round, we compare the first draft assembly results of assembler-race vs. jcvi.


 2 |   15 |   protect
Assemblies of Bordetella hinzii will be reported here1277416151328-296-03CA90-BAL1384L60OH87-BAL007IIContigs Scaffolds

Bioinformatics Education - R language for scientist

 At 2014-07-14 07:49:29 AM - 

R is a language and environment for statistical computing and graphics. It is a GNU project which is similar to the S language and environment which was developed at Bell Laboratories (formerly AT&T, now Lucent Technologies) by John Chambers and colleagues. R can be considered as a different implementation of S. There are some important differences, but much code written for S runs unaltered under R.

R provides a wide variety of statistical (linear and nonlinear modelling, classical statistical tests, time-series analysis, classification, clustering, ...) and graphical techniques, and is highly extensible. The S language is often the vehicle of choice for research in statistical methodology, and R provides an Open Source route to participation in that activity.

One of R's strengths is the ease with which well-designed publication-quality plots can be produced, including mathematical symbols and formulae where needed. Great care has been taken over the defaults for the minor design choices in graphics, but the user retains full control.

 2 |   4 |   public
As well as numerical vectors, R allows manipulation of logical quantities. The elements of a logical vector can have the values TRUE, FALSE, and NA (for “not available”, see below). The first two are often abbreviated as T and F, respectively. Note however that T and F are just variables which are set to TRUE andFALSE by default, but are not reserved words and hence can be overwritten by the user. Hence, you should always use TRUE and FALSE. Logical vectors are generated by conditions. For example > temp <- x > 13sets temp as a vector of the same length as x with values FALSE corresponding to elements of x where the condition is not met and TRUE where it is.The logical operators are <, <=, >, >=, == for exact equality...

Etool support - SFselect

 At 2013-08-27 09:48:40 AM - 

SFselect is a method for classifying genomic regions evolving under positive selection, from those evolving neutrally

SFselect can be used in different ways:

1) Classify polymorphism data using a pre-trained general model that is robust to many different combinations of (s,t) values, while maintaining high power. Barring reliable knowledge of the selective sweep, we recommend using this option.

2)Classify polymorphism data using a pre-trained specific model that is most powerful for a given combination of (s,t) values. These specific models do not generalize as well for other (s,t) values. This option may be used given reliable knowledge of the selective sweep.

3)Classify polymorphism data using your own trained model. This option may be used given reliable knowledge of the demographic history.
 2 |   0 |   public

Etool support - BFB support channel

 At 2013-08-18 08:57:48 AM - 

Breakage-fusion-bridge (BFB) is a mechanism of genomic instability characterized by the joining and subsequent tearing apart of sister chromatids.

When this process is repeated during multiple rounds of cell division, it leads to patterns of copy number increases of chromosomal segments as well as fold-back inversions where duplicated segments are arranged head-to-head.

This software (BFB) facilitates the analysis of BFB mechanism in genomes
Citation: http://www.pnas.org/content/110/14/5546.full

If you have any question of running this tool or any suggestion please feel free to ask in this channel. 

 3 |   1 |   public
- BFB supports two modes :+ Text mode : Submit a text data from text form+ File mode : Submit a big file. The system will notify when finishing. (Sign up or Login if you want to work with files.)Use it at http://etool.me/software/bfb

Tool Request - Request a tool on etool.me

 At 2013-12-24 01:40:38 AM - 

You've just developed a cool bioinformatics tool and you want it to be available on the web. Please raise your request here! 

In order for your tool to be further developed to web portal, you need to provide us:

1) Source code -- your software should be open-source.
2) Link to a published paper.
3) A short video introducing your research project
4) Your software logo (optional).

 6 |   5 |   public
Hi all,It is ready now at http://etool.me/software/psr

Etool support - Sibelia support channel

 At 2013-10-04 08:54:48 AM - 

Sibelia: A scalable and comprehensive synteny block generation tool for closely related microbial genomes.

Ilya Minkin, Anand Patel, Mikhail Kolmogorov, Nikolay Vyahhi, Son Pham. Sibelia: A scalable and comprehensive synteny block generation tool for closely related microbial genomes.

Sibelia will be presented at 13th Workshop on Algorithms in Bioinformatics (WABI2013) in Nice, Sophia Antipolis, France.

Arxiv version is available: http://arxiv.org/abs/1307.7941

If you have any question of running this tool or any suggestion please feel free to ask in this channel. 

 2 |   1 |   public
Release date: 3rd October 2013AuthorsIlya Minkin (St. Petersburg Academic University)Nikolay Vyahhi (St. Petersburg Academic University)Mikhail Kolmogorov (St. Petersburg Academic University)Ekaterina Starostina (St. Petersburg Academic University)Son Pham (University of California, San Diego)IntroductionThis package contains two programs:Sibelia -- "Sibelia" is a tool for finding synteny blocks in closely related genomes, like different strains of the same bacterial species. It takes a set of FASTA files with genomes and locates coordinates of the synteny blocks in these sequences. It also represents genomes as permutations of the blocks.C-Sibelia -- This tool is designed for comparison between two genomes represented either in finished form or...

Etool support - C-Sibelia support channel

 At 2017-06-26 08:54:51 AM - 



C-Sibelia helps in Comparing assemblies to a reference genome. As a result, you will get:

  • A VCF file that describes all the found variants
  • A circos picture visualizes all rearrangements

For your convenience, C-Sibelia also annotates and predicts the effects of these variants on genes using snpEff.


If you have any question of running this tool or any suggestion please feel free to ask in this channel. 
 5 |   6 |   public
Dear Etool support members,Since last week I am trying to run C-Sibelia using two mitochondria genomes size around 85 kb… Still waiting for results…is there is any problem now a days with this tool. Looking forward for your reply.thank you…with regardsVikas

Bioinformatics Education - Python Village

 At 2013-08-14 08:34:19 PM - 

If you are completely new to programming, try these initial problems to learn a few basics about the Python programming language. You'll get familiar with the operations needed to start solving bioinformatics challenges in the Stronghold.
 1 |   2 |   public
In the following examples, input and output are distinguished by the presence or absence of prompts (>>> and ...): to repeat the example, you must type everything after the prompt, when the prompt appears; lines that do not begin with a prompt are output from the interpreter. Note that a secondary prompt on a line by itself in an example means you must type a blank line; this is used to end a multi-line command.Many of the examples in this manual, even those entered at the interactive prompt, include comments. Comments in Python start with the hash character, #, and extend to the...