Bioinformatics CrowdCoding

Whether you publish a problem, or you solve one, the more you contribute at CodersCrowd the more you learn. Technology is moving fast and as a computational biologist you need to be a fast learner. You can read books, follow online tutorials or attend conferences, but the learning curve is not comparable to the one you get from learning by doing. CodersCrowd let you try and be corrected, no matter the complexity or the simplicity of your code is, our community will just bring its expertise to let you know how to do things the right way.

milestones for CodersCrowd

  • First the app was built as a code sharing platform.
  • code exchanged by the usersrunnable, including the most used libraries in Bioinformatics, such as bioperl, biopython, bioconductor

Realtime Programming For Bioinformatics



The ability to accurately model protein structures at the atomistic level underpins efforts to understand protein folding, to engineer natural proteins predictably, and to design proteins de novo. Homology based methods are well established and produce impressive results. However, these are limited to structures presented by and resolved for natural proteins. Addressing this problem more widely and deriving truly ab initio models requires: mathematical descriptions for protein folds; the means to decorate these with natural, engineered or de novo sequences; and methods to score the resulting models.

CCBuilder Tutorial:



Read more


About Symposium

Join us in Farmington, Connecticut Oct. 8 at the inaugural scientific symposium celebrating the opening of The Jackson Laboratory for Genomic Medicine. The focus of JAX Genomic Medicine will be on advancing genomic sciences relevant to human health and disease. The event will showcase the new state of the art 183,500-square-foot research building.

Introducing The Jackson Laboratory

  • Symposium themes include clinical genomics, modeling human diseases, and genomic technologies.

Confirmed speakers include:


Register for the symposium

Registration fee of $50 includes symposium materials and meals provided at the event.

Read more

Within the next two weeks, NCBI will make a major revision to the genomes FTP site. This redesign will expand available content and facilitate data access through an organized, predictable directory hierarchy. The updated site will also provide greater support for downloading assembled genome sequences and/or corresponding annotation data. To give those with automated tools time to update, we plan to maintain the older content and structure of the preexisting /genomes/ FTP site in parallel with the new structure for six months.
  • The new FTP site structure provides a single entry point to access content representing either GenBank or RefSeq data. Advantages of the updated genomes FTP site include the comprehensive provision of data through a single process flow that is reliant on content in NCBI’s Assembly database (which excludes viruses at this time), integration of quality assurance regression tests, and provision of a consistent core set of files for all organisms and assemblies.

Read more

bioinformatics symposium/seminar, Sevilla, Spain, at cicCartuja (CSIC-US)


The XII Symposium on Bioinformatics (XII Jornadas de Bioinformática) will take place on 21-24 September in Sevilla, Spain, at cicCartuja (CSIC-US).Over the last decade, the jornadas have received remarkable submissions from computational groups that have led to new biological discoveries. With the aim of encouraging the participation of younger bioinformaticians, this year symposium's main theme is “Bioinformatics: The New Breed”.


The Raes lab combines large-scale, next-generation sequencing with novel computational approaches to investigate the functioning and variability of the healthy human microbiome at the systems level and study its alteration in disease. In this context, we recently discovered the existence of discrete gut flora types (enterotypes), that are independent of host properties such as nationality, sex or race and are studying the predictive power of microbial markers for various intestinal diseases. In addition, we focus on the development of computational methods for the analysis of (next-generation) sequence data and the investigation of community properties from metagenomics, metatranscriptomics and meta-metabolomics data, which are applied in a wide range of environments (ocean, soil, etc.).

Ben Lehner is an ICREA Research Professor at the EMBL-CRG Systems Biology Program at the Centre for Genomic Regulation. He has a degree and a PhD from the University of Cambridge and was a post-doctoral fellow at the Wellcome Trust Sanger Institute. The main interest of his lab is the genetics and biology of individuals: can we make accurate predictions about how individuals differ from their genome sequences, and why is this often impossible? The lab is funded by the ERC, the EU, and grants from the Spanish and Catalan governments. He was awarded the Banco Sabadell Prize for Biomedical Sciences, the City of Barcelona Prize for Science, the FEBS Anniversary Prize and is an EMBO Young Investigator.

Following a degree in Natural Sciences at Jesus College, University of Cambridge (1993-1996), Nick studied for a Ph.D. with Janet Thornton at UCL (1996-2000) on the basis for specificity of DNA-binding proteins. He then moved to Yale University, USA, as an Anna Fuller Postdoctoral Fellow with Mark Gerstein (2000-2005), where he shifted research focus to genomics with a particular emphasis on yeast transcriptional regulation. He was a Group Leader at the EMBL-European Bioinformatics Institute (2005-2012) in Cambridge and built a computational biology laboratory with an emphasis on genomics and gene regulation. During this time, he joined the Okinawa Institute of Science & Technology as an Adjunct Faculty to establish a small group focused on developmental regulation (2011-present). He has now recently returned to UCL as a Chair in Computational Biology in the UCL Genetics Institute and holds a joint appointment as a Senior Group Leader at the Cancer Research UK London Research Institute. His laboratory will be joining the Francis Crick Institute in 2015.

Mihaela Zavolan is Professor in the Bioinformatics Division of the Biozentrum Basel. She leads a group whose focus is the computational study of the regulatory networks leading to tissue-specific expression of protein forms. The current projects in her lab are aimed at development of computational tools for the discovery of transcription regulatory modules, of splice regulatory signals, and of small regulatory RNAs.

Abstract Submission

Abstract topics

  • Metagenomics (A)
  • Integrative Biology (B)
  • Medical Informatics (C)
  • Phylogeny/Evolution (D)
  • Structure/function (E)
  • Highlights (H)
  • Student Symposium (S)
Among these topics, you will be required to first select the topic most closely related to your work and then a second topic also related to your work. If you submit a Highlight, you must upload the full article.

Number of Submissions

  • Two abstract submissions allowed per presenting author.

Title and Abstract Length

  • The abstract title is limited to 150 characters (aprox. 20 words). Abstract body should be no more than 2500 characters (aprox. 350 words), not including the title.

Abstract Presentation

  • Only a limited number of oral presentations are possible. The scientific committee will decide whether your work will be presented via oral or poster. During your registration, please indicate if you are happy to present your work as an oral or as a poster.

Abstract Publication

  • Approved abstracts will be included in the proceedings

Read more

bioinformatics drug discovery


Click2Drug contains a comprehensive list of computer-aided drug design (CADD) software, databases and web services.These tools are classified according to their application field, trying to cover the whole drug design pipeline.

What is CADD

List of CADD software, databases and web services Provided by Click2Drug:


Chemical databases

  • PubChem Mobile. Free application to search PubChem databases using chemical names, synonyms, and keywords. For Android.
  • Approved Drugs. The Approved Drugs app contains over a thousand chemical structures and names of small molecule drugs approved by the US Food & Drug Administration (FDA). Structures and names can be browsed in a list, searched by name, filtered by structural features, and ranked by similarity to a user-drawn structure. The detail view allows viewing of a 3D conformation as well as tautomers. Structures can be exported in a variety of ways, e.g. email, twitter, clipboard. For iPad and iPhone. Developed by Molecular Materials Informatics, Inc.
  • ChemSpider Mobile. Allows searching the ChemSpider chemical database, provided by the Royal Society of Chemistry. Compounds can be searched by structure or by name, and browsed within the app. Results can be examined by jumping to the web page. Search structures are drawn using the powerful MMDS molecular diagram editor. For iPad. Provided by Molecular Materials Informatics, Inc.
  • SPRESImobile. iPod, iPhone and iPad application providing direct access to ChemReact, a subset of the SPRESI structure and reaction database, which contains more than 400,000 unique reaction types and the related references. Developed by InfoChem.
  • MORE. (MObile REagents). Mobile app, for iphone, ipad and android, which gives access to over 9 million molecules and 16 million chemical product variations offered by 56 different suppliers. Can search reagents by name, formula or by drawing a chemical structure. It is possible to limit the search to specific suppliers, bookmark the search results, and export small sdfiles. Allows converting a picture of a chemical structure taken from the iPhone camera into a structurally searchable molecule using OSRA (Optical Structure Recognition Application).
  • iKinase Universal. iPad/iPhone application providing sample structure activity data from Eidogen-Sertanty's Kinase Knowledgebase (KKB). Exists in a Pro version (iKinasePro).

Chemical structure representations

2D drawing

  • ChemDraw for iPad. iPad application to create, edit and share publication-quality chemical structures with just the touch of a finger, based on the world’s most popular chemical drawing software, ChemDraw. Provided by PerkinElmer, Inc.
  • ChemDoodle Mobile. Free iPhone companion to ChemDoodle. ChemDoodle Mobile is a calculator for drawn organic structures. There are four main windows: Draw, Calculate, Spectra and Help. The Draw window shows a typical ChemDoodle sketcher, where you can draw and store your structures. The Calculate page calculates properties and the Spectra page simulates NMR spectra. All spectra are interactive. The Help page contains a thorough help guide. Provided by iChemLabs.
  • Chirys Draw. Application for drawing publication-quality molecular structures and reactions. Designed from the ground up for the iPad. Developed by Integrated Chemistry Design, Inc.
  • Chirys Sketch. Application for drawing publication-quality molecular structures and reactions, for iPhone and iPod Touch. Developed by Integrated Chemistry Design, Inc.
  • Mobile Molecular DataSheet. Allows viewing and editing chemical structure diagrams on an iPhone, iPod or iPad. Molecules are organized in collections of datasheets. Individual molecules, or whole datasheets, can be shared via iTunes or sent by email, using the standard MDL MOL and SDfile formats, which allows the data to be integrated into any external workflow. Provided by Molecular Materials Informatics, Inc.
  • SAR Table. Application designed for creating tables containing a series of related structures, their activity/property data, and associated text. Structures are represented by scaffolds and substituents, which are combined together to automatically generate a construct molecule. The table editor has many convenience features and data checking cues to make the data entry process as efficient as possible. For iPad. Provided by Molecular Materials Informatics, Inc.
  • Molprime+. Chemical structure drawing tool based on the unique sketcher from the Mobile Molecular DataSheet. Can send structure data via email, open structures from email or web, create graphical images or Microsoft Word documents with embedded structure graphics, calculate properties based on structures and use structures to search Mobile Reagents and ChemSpider. Provided by Molecular Materials Informatics, Inc.
  • StructureMate. Portable chemical dataset viewer for iPad, for browsing SAR reports, chemical catalogs, custom-made databases, and physical property references. Provided by Metamolecular, LLC.
  • Elemental. Chemistry sketch for iphone and ipad. Developed by Dotmatics Limited.
  • ChemJuice. Molecular drawing software for iPhone. Developed by IDBS.
  • ChemJuice Grande. Molecular drawing software for iPad. Developed by IDBS.
  • MolPad. Free chemical structure drawing application. It can draw structures from scratch or load them from ChemSpider and modify them. Structures can be emailed in Molfile format. For Android.
  • DCE ChemPad. Free application to draw chemical structures and calculate molecular weight, molecular formula and to send the molfile. It shows the capabilities of the Dendro Chemical Editor control for Android to build chemistry-aware mobile applications. For Android.
  • TouchMol Mobile App. Tool for drawing chemical and biological structures. Allows Copy/Paste to ChemDraw, ISIS/Draw, SciFinder and Word. Provides name-to-structure. For Windows 8 mobile devices. Provided by Scilligence.

2D drawing online

  • OLN JSDraw. Javascript libary you can display and draw chemical structures in web pages, which works cross browser, including IE, Firefox, Safari, Opera and Chrome, crose platform, including Window, Mac, Linux, and even iPhone, Android and other mobile devices. Free for education. Provided by Scilligence.

3D viewers

  • GLmol. Free and open source 3D molecular viewer based on WebGL and Javascript. GLmol runs on newer versions of Firefox, Chrome, Safari or Opera. Internet Explorer is not supported. GLmol also runs on Sony Ericsson's Android devices which support WebGL and WebGL enabled safari in iOS.
  • iMolview. Application to browse and view in 3D protein and DNA structures from Protein Data Bank, and drug molecules from DrugBank For iPhone and iPad. Provided by Molsoft.
  • PyMOL on the iPad.. High-performance 3D molecular visualizer, designed from the ground up for the iPad. it can search and download data from the PDB, PubChem, Dropbox, or an own secure custom PyMOL enterprise server. Provided by Schrödinger.
  • RCSB PDB.. The RCSB Protein Data Bank (PDB) mobile app is the official mobile app of the RCSB PDB. It provides fast, on-the-go access to the RCSB PDB resources. The app enables the general public, researchers and scholars to search the Protein Data Bank and visualize protein structures using either a WiFi or cellular data connection.
  • Ball&Stick. High-quality molecular visualization app for the iPad, iPhone and iPod Touch. Provided by MolySym.
  • CueMol for iOS. Interactive macromolecular viewer for structural biologists. CueMol viewer allows the users to open and view the scene files made by the desktop version of CueMol, and the Protein Data Bank (PDB) format files, as well.
  • 3D Molecules Edit&Drill. Application designed to enable students and professionals to build, construct, modify and examine molecules in 3D. Allows the users to open and view molecules in SDF format files, for example, from NCBI's PubChem. Developed by Virtualnye Prostranstva LLC.
  • Chem3D for iPad. Chem3D for iPad enables scientists to view and manipulate 3D images of chemical and biochemical structures. Re-imagined for the iPad, the Chem3D app features a facile user interface to manipulate images using common touch, pinch and swipe gestures. Provided by PerkinElmer, Inc.
  • CMol. Interactive 3D molecular viewer designed specifically for the iPad, iPhone and iPod touch. CMol allows the user to open and view PDB files with complete control over the representations and colours used for individual chains, residues and atoms.
  • Molecules. Free application for iPhone and iPad, for viewing three-dimensional renderings of molecules and manipulating them using your fingers. You can rotate the molecules by moving your finger across the display, zoom in or out by using two-finger pinch gestures, or pan the molecule by moving two fingers across the screen at once. These structures can be viewed in both ball-and-stick and spacefilling visualization modes.
  • iMolecular Builder. The IMoleBuilder is an application that can view, edit and build molecules in 3D. For iPhone.
  • iPharosDreams. Molecular visualization app for iPad to perform in-silico drug discovery. Downloads protein structure files from Protein Data Bank, displays 3D molecules, touch, rotation, zoom in/out. Hierarchy structure of molecules is shown with a table that select components in a protein and related things. It can generate pharmacophores and analyze 3D protein-ligand interaction of biological macromolecules for in-silico drug discovery. Allows selecting a ligand from a protein and generate a binding site from the selected ligand. Can generate receptor based pharmacophores and get inspiration. Developed by EQUISnZAROO CO., LTD.
  • Jmol Molecular Visualization. Free Jmol for Android tablets.
  • NDKmol. Free molecular viewer for Android.
  • Molecule Viewer 3D. Opens most common 3D molecule file formats saved on a SD card or found in a library of 243 included molecules. For Android.
  • 3D Molecule View. 3D molecule viewer. For Android.
  • Atomdroid. Free computational chemistry tool. It can be used as a molecular viewer/builder and contains local optimization and Monte Carlo simulation features. For Android.
  • Atom 3D. Free application to visualize molecules and crystal structures in 3D using the touchscreen to rotate and zoom. Includes 19 sample structures. Supports XYZ files and some protein data bank (PDB) files. For Android.
  • PDBs. Free application for molecular graphics visualization from PDB files. For Android.
  • PDB View 3D. Application for molecular graphics visualization from PDB files. For Android.

File format Converters

  • MolEngine. .NET Cheminformatics Toolkit completely built on Microsoft .NET platform. By using Mono, MolEngine can run on other platform, such as Mac, Linux, iPad. Distributed by Scilligence.

Molecular Modeling


  • iHyperChem Free Version. Free Version of iHyperChem for iPad. Provided by HyperChem.
  • iSpartan. iSpartan is a versatile app for molecular modeling on the iPad, iPhone, and iPod Touch. Molecules are created by two-dimensional sketching and converted into a three-dimensional structure. Low-energy conformations can then be calculated and their geometries be queried. A database of 5,000 molecules (a subset of the Spartan Spectra and Properties Database, SSPD) can furthermore be accessed to obtain NMR and IR spectra, molecular orbitals, electrostatic potential maps, and other atomic and molecular properties. The database can be searched for substructures. Developed by Wavefunction, Inc.

Homology Modeling

Web services and databases

  • iProtein. iPad application providing access to the Eidogen-Sertanty's Target Informatics Platform (TIP).

ADME Toxicity


  • SimCYP for iPhone.. The SimCYP Population-based ADME Simulator is a platform for the prediction of drug-drug interactions and pharmacokinetic outcomes in clinical populations. For iPhone. Distributed by SimCYP.

Read more


What Is Google Genomics?

Google Genomics provides an API to store, process, explore, and share DNA sequence reads, reference-based alignments, and variant calls, using Google's cloud infrastructure.
  • Store alignments and variant calls for one genome or a million.
  • Process genomic data in batch by running principal component analysis or Hardy-Weinberg equilibrium, in minutes or hours, by using parallel computing frameworks like MapReduce.
  • Explore data by slicing alignments and variants by genomic range across one or multiple samples -- for your own algorithms or for visualization; or interactively process entire cohorts to find transition/transversion ratios, allelic frequency, genome-wide association and more using BigQuery.
  • Share genomic data with your research group, collaborators, the broader community, or the public. You decide.
  • Google Genomics is implementing the API defined by the Global Alliance for Genomics and Health for visualization, analysis and more. Compliant software can access Google Genomics, local servers, or any other implementation.


Google Genomics fundamentals:

Interacting with Google Genomics:

Read more


About ENCODE Data

The Encyclopedia of DNA Elements (ENCODE) Consortium is an international collaboration of research groups funded by the National Human Genome Research Institute (NHGRI). The goal of ENCODE is to build a comprehensive parts list of functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells and circumstances in which a gene is active.
  • ENCODE data are now available for the entire human genome.
  • All ENCODE data are free and available for immediate use via :


  • Search for displayable tracks and downloadable files
  • This page contains links to search tools for finding tracks displayed in the browser or downloadable files that are part of the ENCODE project. All tracks and files for ENCODE data are released as part of the ENCODE production phase (September 2007-present). For bulk download, retrieval by FTP is recommended along with rsync. All ENCODE data are covered by the ENCODE data release policy.

Download of data files

  • This page contains links to directories containing raw and processed data released as part of the ENCODE production phase (September 2007 - December 2012). Formats are described on the File Format FAQ. For bulk download, retrieval by FTP is recommended along with rsync.



Data mining

Data mining

Read more

Advance Praise for Bioinformatics Algorithms:

“This lively and unique text on bioinformatics motivates algorithmic thinking with an abundance of up-to date examples from molecular biology.” — Michael Waterman, University Professor of Biological Sciences, Mathematics, and Computer Science, University of Southern California
“A refreshing, original approach to teaching the foundations of bioinformatics, this textbook builds the reader’s comprehension by combining hands-on exercises with illuminating biological stories and mathematical rigor.” — Ron Shamir, Sackler Chair in Bioinformatics, Computer Science Department, Tel Aviv University



Chapter 1: Where in the Genome Does DNA Replication Begin?

Chapter 1: Where in the Genome Does DNA Replication Begin?

  • The Search for Hidden Messages in the Replication Origin (Part 1)

Chapter 2: How Do We Sequence Antibiotics?

  • The Discovery of Antibiotics

Chapter 3: Which DNA Patterns Play the Role of Molecular Clocks?

  • From Implanted Patterns to Regulatory Motifs (Part 1)

Chapter 4: How Do We Assemble Genomes?

  • What Is Genome Sequencing?

Chapter 5: How Do We Compare Biological Sequences?

  • From Sequence Comparison to Biological Insights

Chapter 6: Are There Fragile Regions in the Human Genome?

  • Transforming Men into Mice

Chapter 7: How Do We Locate Disease-Causing Mutations?

  • Why Do We Map Reads?

About The Authors

Phillip Compeau is a Ph.D. candidate in the University of California, San Diego (UCSD) Department of Mathematics. He is an Achievement Rewards for College Scientists Scholar. He holds Master’s degrees from Cambridge University and UCSD in addition to a Bachelor’s degree from Davidson College. He researches the combinatorics of genome rearrangements and is passionate about the future of education, having cofoundedRosalind with Nikolay Vyahhi. A retired tennis player, he dreams of one day going pro in golf.
Pavel Pevzner is Ronald R. Taylor Professor of Computer Science at the University of California, San Diego. He holds a Ph.D. from Moscow Institute of Physics and Technology, Russia. He is a Howard Hughes Medical Institute Alumnus Professor (2006), an Association for Computing Machinery Fellow (2010), and an International Society for Computational Biology Fellow (2012). In addition to Bioinformatics Algorithms: An Active Learning Approach, he has authored the textbooks Computational Molecular Biology: An Algorithmic Approach (2000) and An Introduction to Bioinformatics Algorithms (2004) (jointly with Neil Jones).

Read more

MARI themes

{facebook#} {twitter#} {google#}
Powered by Blogger.