VT Genome analysis and protein folding support

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General Project Information

  • Leader: Afonso Duarte (ITQB-UNL, Portugal)
  • Meetings: via teleconference
  • Mailing List: vt-gapf(_at_)mailman.egi.eu
  • Status: Implementation
  • Start Date: 24-05-2014
  • End Date: 20-05-2015
  • Meetings :

From implementation phase: 22nd July 2014; 17th September 2014; 8th October 2014; Final VT project F2F meeting during the EGI Conference in Lisbon 20th May at 13:30

From scoping phase: 22th January 2014; 5th February 2014; 20th February 2014; 12th March 2014; 27th March 2014.


Motivation

The researchers working with applications in the fields of Protein Structural Biology and Sequence Analysis (Protein/DNA/RNA) are growing communities within the EU research map. The setup of several FP7 projects and the increasing number of National and European infrastructures in these fields is self-evident (e.g. national ELIXIR nodes, PATHSEEK, NGS-PTL, RESPONSIFY projects).

Within the European Grid Infrastructure several VRCs (like WeNMR and LSGC) and VOs (like enmr.eu, biomed, …) have been setup to tackle the computational needs of these fields of science. However the information on how new users can approach and use such applications and tools is disperse and not obvious to access for users that work in the Biological Sciences field and are inexperienced with large-scale distributed computing systems.

The goal of this VT is to bridge the panoply of powerful tools, applications, workflows and knowledge existing within EGI and the end-users. This will be done via a) the setup of new training activities and outreach documents based on existing applications and b) the identification and integration of new tools and application in EGI that can attract new users to the infrastructure by advancing science. This VT also aims at triggering the setup of new knowledge networks within the users and EGI therefore potentiating future collaboration in research projects (e.g. future Horizon 2020 proposals).



Objectives

The beneficiaries of GAPF VT are Protein Structural Biology and Sequencing (Protein/DNA/RNA) communities.
The main objective of the VT is to increase awareness amongst the community of the existing services and applications of EGI that fall inside their expertise area, and to increase the attractiveness of EGI for researchers of these fields by the further development of the e-infrastructure.
The following supporting aims will help to achieve the major goal.


1. Identify tools available in the EGI e-infrastructure relevant for the VT interested community.

2. Identify reusable tools and scientific applications relevant for the VT interested community not yet supported by EGI, and make these available on the EGI production infrastructure.

3. Develop outreach materials to disseminate relevant applications to the target community.

4. Identify synergies (knowledge networks) within the users in order to increase the EGI usage experience and increase the number of users.

5. Organize training and promotional sessions to disseminate the services, tools and applications to potential users.

Tasks


T1 - Identify relevant applications, inside the scope of the VT, that are already available on the EGI e-infrastructure;

T2 - Identify relevant tools, applications, inside the scope of the VT, that are not yet available on EGI e-infrastructure, but that would benefit from the integration;

T3 - Promote the outcome of the VT to the target communities.

Members

EGI.eu

  • Gergely Sipos, EGI.eu, Netherlands
  • Nuno Ferreira EGI.eu, Netherlands
  • Neasan O'Neill EGI.eu, Netherlands

Portugal

  • Afonso Duarte, EGI Champion
  • João Pina, LIP, IberGrid

Greece

  • Fotis E. Psomopoulos, EGI Champion
  • Kostas Koumantarosm, GRNet

Italy

  • Daniele Cesini, INFN
  • Alessandro Constantini, INFN

France

  • Johan Montagnat, CNRS, LSGC
  • Tiphaine Martin, KCL

Spain

  • Jesus Marco de Lucas, CSIC
  • Beatriz Ranz Ribeiro , CSIC
  • Ignacio Blanquer, UPVLC

Finland

  • Kimmo Mattila, CSC

Germany

  • Konrad Förster, IMIB

UK

  • Rafael Jimenez, ELIXIR


The Netherlands

  • Alexandre Bonvin, WeNMR


Others ? YOU ! (if interested in this Virtual Team contact us - aduarte(+at+)itqb.unl.pt)

Resources


Progress

  • List of tools used/required by the sequencing and protein folding communities (see table below).

To add/change entries please use: https://docs.google.com/spreadsheet/ccc?key=0Ama69JoAAogvdHFzQi1UamwxN0MtVS1GUEV4ZmVGWXc&usp=sharing. If you don't have permission to do so please let us know!



Output: Community Use Cases

READemption

READemption is a pipeline for the computational evaluation of RNA-Seq data. The use case consists in running the analysis workflow on the EGI Cloud Federation. (Concluded use case)

Konrad Förstner (University of Würzburg, Germany)

Application: http://pythonhosted.org/READemption/


Webinar on READemption will take place on the 27th November 2014 (access here: https://indico.egi.eu/indico/conferenceDisplay.py?confId=2345 ).

The webinar will be recorded and a video will subsequently be made available via the EGI YouTube channel: https://www.youtube.com/user/EuropeanGrid .


Trufa

TRUFA (Transcriptomes User-Friendly Analysis) is a webserver designed to help researchers in genomics to perform de novo RNA-seq analysis. The goal is to exploit Cloud Federation resources from the TRUFA portal. (Ongoing Use Case)

Jesus Marco de Lucas (Instituto de Fisica de Cantabria, Spain)

Application: https://trufa.ifca.es/web

FedCloud Wiki: https://wiki.egi.eu/wiki/FedCloudTRUFA


Chipster

Chipster is a user-friendly analysis software for high-throughput data. It contains over 300 analysis tools for next generation sequencing (NGS), microarray, proteomics and sequence data. Chipster's client software uses Java Web Start to install itself automatically, and it connects to computing servers for the actual analysis. Chipster is open source and the server environment is available as a virtual machine image. (Ongoing Use Case)

Application: http://chipster.csc.fi/

FedCloud Wiki: https://wiki.egi.eu/wiki/FedCloudChipster


RSAT

RSAT provides a series of modular computer programs specifically designed for the detection of regulatory signals in non-coding sequences. (Ongoing Use Case)

Application: http://rsat.ulb.ac.be/

Fedcloud Wiki: https://wiki.egi.eu/wiki/FedCloudRSAT



List of tools used/required by the sequencing and protein folding communities

This list is a contribution from the different NGIs, users, developers, ...

If want to add/change entries please use the file (https://docs.google.com/spreadsheet/ccc?key=0Ama69JoAAogvdHFzQi1UamwxN0MtVS1GUEV4ZmVGWXc&usp=sharing).

If you don't have permission to do so please let contact us !

P.S.: This is a work in progress table

 

Name type of tool (Application, workflow...) Target Community(ies)

                                                                                                                              

Description      
                                                                

Available in AppDB? AppDB URL Available online ? website Developer Open source










Gromacs Application Protein structure, protein folding and protein dynamics Performs molecular dynamics i.e calculate the Newtonian equations of motion for systems with hundreds to millions of particles. GROMACS can work with different biochemical molecules (e.g. proteins, lipids and nucleic acids) yes https://appdb.egi.eu/store/software/gromacs.wenmr yes http://www.gromacs.org/ http://www.gromacs.org/ yes
BLAST Application Bioinformatics, General Application, Basic Local Sequence Alignment BLAST is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences. yes https://appdb.egi.eu/store/software/blast



BiG (BLAST in Grids) Application Bioinformatics, General Application, Basic Local Sequence Alignment To draw a comparison by BLAST between all sequences of prokaryotes, fungi, plants and animals
The objective of this project, to run an application on the Grid infrastructure provided by the e-Science network, is to be able to launch BLAST processes in that infrastructure. More precisely, it is to draw a comparison by BLAST between all sequences of prokaryotes, fungi, plants and animals. The results are then analyzed using scripts to estimate the degree of horizontal transfer of genes between prokaryotes and plants.
To do so, those proteins that are found in prokaryotes and plants but not in animals will be identified, using different similarity thresholds to consider to what extent the similarity between two proteins implies a common origin or not.

yes https://appdb.egi.eu/store/software/big.blast.in.grids



BWA Burrows-Wheeler Aligner Application Bioinformatics, General Application, Next Generation Sequence Assembling Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome.
Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. It implements two algorithms, bwa-short a nd BWA-SW. The former works for query sequences shorter than 200bp and the latter for longer sequences up to around 100kbp. Both algorithms do gapped alignment. They are usually more accurate and faster on queries with low error rates.

yes https://appdb.egi.eu/store/software/bwa.burrows.wheeler.aligner



VELVET Application Bioinformatics, General Application, Next Generation Sequence Assembling Sequence assembler for very short reads
Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom.
Velvet currently takes in short read sequences, removes errors then produces high quality unique contigs. It then uses paired-end read and long read information, when available, to retrieve the repeated areas between contigs.

yes https://appdb.egi.eu/store/software/velvet



SOAP-denovo Application Bioinformatics, General Application, Next Generation Sequence Assembling SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes.
The program is specially designed to assemble Illumina GA short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way.

yes https://appdb.egi.eu/store/software/soap.denovo



ClustalW-MPI Application Bioinformatics, General Application, Multiple Sequence Alignment ClustalW parallel implementation
ClustalW is a tool for aligning multiple protein or nucleotide sequences. The alignment is achieved via three steps: pairwise alignment, guide-tree generation and progressive alignment. ClustalW-MPI is a distributed and parallel implementation of ClustalW. All three steps have been parallelized to reduce the execution time.

yes https://appdb.egi.eu/store/software/clustalw.mpi



CLUSTALW Application Bioinformatics, General Application, Multiple Sequence Alignment ClustalW is a program to perform multiple alignment of nucleic acid and protein sequences yes https://appdb.egi.eu/store/software/clustalw.mpi



MAFFT Application Bioinformatics, General Application, Multiple Sequence Alignment Multiple Alignment using Fast Fourier Transform
MAFFT is a multiple alignment program for amino acid or nucleotide sequences

yes https://appdb.egi.eu/store/software/mafft



MUSCLE Application Bioinformatics, General Application, Multiple Sequence Alignment MUltiple Sequence Comparison by Log-Expectation
MUSCLE is public domain multiple alignment software for protein and nucleotide sequences

yes https://appdb.egi.eu/store/software/muscle



HMMER Application Bioinformatics, General Application, Multiple Sequence Alignment Profile hidden Markov models (profile HMMs) can be used to do sensitive database...
Profile hidden Markov models (profile HMMs) can be used to do sensitive database searching using statistical descriptions of a sequence family’s consensus. HMMER is a freely distributable implementation of profile HMM software for protein sequence analysis

yes https://appdb.egi.eu/store/software/hmmer



MrBayes Application Bioinformatics, General Application, Phylogenetics A program for the Bayesian estimation of phylogeny
The reconstruction of the evolutionary history of a group of organisms (phylogeny) is used throughout the life science, as they offer a structure around which to organize the knowledge and data accumulated by researchers. The inference of phylogenies with computational methods is widely used in medical and biological research and has many important applications, such as gene commonly prediction, drug discovery and conservation biology. The most commonly used methods to infer phylogenies include cladistics, phenetics, maximum likelihood and Markov Chain Monte Carlo based Bayesian inference.
These last two depend upon a mathematical model describing the evolution of characters observed in the species included and are usually used for molecular phylogeny where the characters are aligned nucleotide or amino acid sequence. Due to the nature of Bayesian inference, the simulation can be prone to entrapment in local optima. To overcome this problem and achieve better estimation, the MrBayes program has to run for millions of iterations (generations) which require a large amount of computation time.
For multiple sessions with different models or parameters, it will take a long time before the results can be analyzed and summarized. Since the phylogenetic tools are widely used by bioinformatics community, a Grid service for the parallelised version of MrBayes application has been deployed in order to allow bioinformatics to perform phylogenetic studies on a large scale.

yes https://appdb.egi.eu/store/software/mrbayes



CD-HIT-Grid Application Bioinformatics, General Application, Sequence Analysis Protein clustering on the Grid with CD-HIT
CD-HIT performs protein clustering on a protein or genome sequence database. This consists in removing redundant sequences at a given sequence similarity level and generating a new database with the representatives only. As protein and genome databases are growing up day after day, the clustering process on interesting datasets in a single machine is not feasible due to memory constrains. A Grid environment allows an adaptive database distribution in order to optimize its overall analysis. This activity was proposed by CNIO (Spanish National Cancer Research Centre) and started in the context of the BioGridNet Program

yes https://appdb.egi.eu/store/software/cd.hit.grid



InterProScan Application Bioinformatics, General Application, Sequence Analysis InterProScan is a tool that combines several types of analysis in order to assign one or more functional signatures to a particular protein.
InterProScan is a tool that combines several types of analysis in order to assign one or more functional signatures to a particular protein. It is implemented as a wrapper for some applications that can be executed simultaneously and combined in a computational analysis.
The application was ported within the framework of the FP7 EDGeS project

yes https://appdb.egi.eu/store/software/interproscan



Grid Bio Portal (GISELA) Platform Bioinformatics, Sequence Analysis Grid Portal of Bioinformatics Applications
The application consists on a Grid Portal in which different bioinformatics applications can be deployed. Different Grid services implement basic tools such as multiple alignments, Phylogenetics inference, etc, which run on a Grid infrastructure, along with more complex compound workflows that implement widely used analysis sequences.
The portal will provide authentication, load balancing, session management, workflow, user interface, reliability, fault tolerance, data management and accounting. This software layer will increase the productivity of software production cycle and will offer a uniform framework to host Grid services.
The portal will run on a computer provided of a Grid User Interface, acting as a bridge between the Web and the Grid sides. It makes use of myproxy servers and all the other global Grid Services (data catalogue, resource brokering, file transfer, etc.).

yes https://appdb.egi.eu/store/software/grid.bio.portal.gisela



EMBOSS_in_JST Application, Platform Bioinformatics, Sequence Analysis The European Molecular Biology Open Software Suite in the JST framework
EMBOSS, ”The European Molecular Biology Open Software Suite” is a free Open Source software analysis package well established in the world-wide bioinformatics community. The tool has been adapted to be executed on the EGEE grid infrastructure within the JST framework in order to perform large scale analyses. Compared to other porting of the EMBOSS package on the GRID environment such as GrEMBOSS (http://cimi.ccg.unam.mx/ccg-OrganicG/en/GrEMBOSS), a gridified version of EMBOSS developed inside the EELA project, EMBOSS_in_JST appears to be well performing in the management of large data flow. The validity of the EMBOSS_in_JST approach was validated on a case study on Viroids. They are circular RNAs infecting plants. They show compact secondary structures and are unable to code for any protein. Infectivity of these RNAs exclusively relies on their ability to interact directly with host factors (proteins and/or RNAs) and to redirect cellular machinery and biosynthetic pathways for their replication and spread in the host. Viroids accomplish this aim likely mimicking some host RNA structural property. Therefore, viroid RNAs may unveil structural motives with functional properties also contained in cellular RNAs. Bioinformatics approaches in viroid research are impaired by the fact that the complete genome of most natural viroid hosts is still unknown. To overcome this difficulty we decided to run a secondary structure analysis on sub-sequences of the whole plant sequence data set available in EMBL. We analysed as a first test 231’000 intron regions for the secondary structure of interest by using the vrnalfold algorithm (search for local folding patterns) from the EMBOSS/EMBASSY package.

yes https://appdb.egi.eu/store/software/emboss.in.jst






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