The big move and other news!

Blog
Hi everyone! It's been a while since the last post and a lot has changed! Yesterday we celebrated the move of our UK office to a newly developed tech hub in central Cambridge. Our new neighbours include Docker and Electric Imp and we're very excited...

Genestack moves to a bigger space and plans to double in size

Press releases
  Genestack is expanding and moving to a new tech hub in central Cambridge. The company is expecting to double in size in 2017 Cambridge, 17 November 2016 … Genestack, a bioinformatics company developing a next generation platform accelerating gen...

Visit Genestack at ASHG 2016 in Vancouver!

Blog
Hi everyone! The annual ASHG Meeting is one week away. This time, the world’s largest gathering of human genetics professionals is taking place in Vancouver.  We would like to invite you all to come visit us at our booth #935 to get a chance to ...

Meet our new Bioinformatics Software Developer!

Blog
Hi everyone, I’m Eleonora! I have recently joined Genestack as a Bioinformatics Software Developer. Just a few months back I have graduated from University of Cambridge with a PhD in Mathematical Genomics and Medicine. During my PhD I have performed a...

Meet our new Business Development intern!

Blog
Hi! I’m Nemunas, I’ve recently joined Genestack as a Business Development intern. I graduated from the Biological Natural Sciences course at the University of Cambridge a few months ago. In my studies I initially focused on wet-lab work, but a ser...

How to...choose a reference genome?

Blog
Hi everyone! As you know, recently our team has been working hard to put together an Ultimate Guide to Genestack Platform. This guide consists of a general introduction to bioinformatics and the basics of sequencing analysis, as well as a comprehensive...

How to...choose a mapper?

Blog
Hi everyone, We have some news for you: recently our team has been working hard to put together an Ultimate Guide to Genestack Platform. This guide consists of a general introduction to bioinformatics and the basics of sequencing analysis, as well as a...

Genestack presentation at the Festival of Genomics Boston 2016

Blog
Hello everyone! Festival of Genomics Boston is a conference that brings together doctors, researchers and various companies operating in the field of genomics to discuss the latest advancements in the field, its future and the current bottlenecks. We l...

Platform Release 34 – What's New?

Platform news
Hello everyone, It's time for our next release! It comes with a new app, several new important features and interface improvements as well as bug fixes and performance enhancements. New app for data export We released a new Manage app: Export Data fo...

Building pipelines and reproducing results

Blog
Hello! We are in the process of preparing something that we're sure our users will love: an Ultimate Guide to Genestack Platform. We built Genestack to be intuitive and easy to use, but we recognize the fact that some of our users don't have much exper...

Platform Release 33 – What's New

Platform news
Hello everyone, We're excited to announce our next release - Platform Release 33! It comes with several new important features and interface improvements as well as bug fixes and performance enhancements. Shortcuts menu First of all, as you might ...

Developing NGS-based assays for haematological cancer research

Blog
Hello everyone! My name is Yvonne and I am currently a Research Associate at the Cancer Molecular Diagnostic Laboratory (CMDL), University of Cambridge. I joined Genestack as part of an Industrial Exchange Fellowship that is funded by the Medical Research...

Sequencing and Bioinformatics– where is the medical revolution?

Blog
This article was originally published in Splice on 9th of February 2016. You can find the original version here. The challenges of bioinformatics Let’s take a look back at how much genome sequencing used to cost during the span of the last 15 years. In ...

Looking back at Bio-IT Conference 2016

Blog
Last week we went to Boston for the Bio-IT World Conference 2016. During three days of the conference we met loads of interesting people, listened to exciting talks and had a chance to see what other companies are up to. Each day of the conference ...

Genestack to Collaborate with CMDL

Press releases
Genestack to Collaborate with Cancer Molecular Diagnostic Laboratory Collaboration Will See Genestack Platform Used in Clinical Care Cambridge, 11 April 2016 … Genestack, the developer of a next generation enterprise platform for genomics research and d...

Honourable Mention at Bio-IT Best of Show Awards

In the media
The Best of Show awards program at the Bio-IT World Conference and Expo recognizes the top innovative product solutions for the life sciences industry on display at the conference in Boston. New products released or significantly improved in the past year...

Bio-IT World 2016 Best of Show Finalist

Blog
We are very proud to announce that Genestack is a Best of Show finalist in the Informatics Tools & Data Analytics category for our Genestack Platform! It is an award that identifies exceptional innovation in technologies used by life science pr...

New Agri-Genomics Tools Available on Genestack Platform

Press releases
  Cambridge, 7 March 2016 … Genestack, the developer of a next generation enterprise platform for genomics research and development, will be making new tools for agri-genomics available on its platform for early adopters as part of a project with ...

Genestack and Rothamsted Research Kick-off Agrigenomics Collaboration

Blog
We have kick started our Innovate UK funded collaborative project with Rothamsted Research, a major UK agri-genomics research centre and the longest running agricultural research station in the world. Our objective is to combine the Genestack platform wit...

New Research Identifies Multiple Gene Defects Involved in Fungal Asthma

Press releases
29 February 2016 … Researchers have identified a number of genetic defects or alterations that can lead to an increased susceptibility to fungal asthma. The discovered genetic variants are related to an increased risk of damage to the lining cells of the ...

New visualisation and clustering methods for single-cell RNA-seq data

Platform news
There are many different tools and methods for visualising the structure of high-dimensional single-cell RNA-seq data as well as for identifying subpopulations of cells. Most of these methods focus on keeping dissimilar samples far away from each other. H...

Genestack Forum 2.0

Blog
Hi everyone! We decided to bring our Genestack Forum back to life. It's a perfect place for you to ask questions about Genestack: anything from how to use our bioinformatics platform to questions about documentations on writing apps. Other users of ...

Whole exome sequencing data analysis on Genestack platform

Blog
As one of the widely used targeted sequencing method, whole exome sequencing (WES) has become more and more popular in clinical and basic research. Albeit, the exome (protein-coding regions of the genome) makes up ~1% of the genome, it contains about 85% ...

Our team is growing!

Blog
Hi, I’m Steph! I joined Genestack at the beginning of this year, having had less experience than most in actual programming. But within a month, I’ve already learnt so much about bioinformatics and have been mentored extremely well. I completed my M...

Looking back at the Festival of Genomics 2016

Blog
We were very excited to attend the Festival of Genomics, held in London on 19th-21st of January 2016. Two days of the conference were filled with interesting workshops, stimulating  presentations and inspiring people. It was a valuable opportunity ...

Genestack at the Festival of Genomics

Blog
Festival of Genomics London is five days away! Before the event starts, let's take a look at what Genestack has been up to during the last year and what we'll present at the Festival. Genestack was founded in 2012 by Dr. Misha Kapushesky, previousl...

Getting started on Genestack Platform

Blog
In this tutorial, we'd like to introduce you to the core features of Genestack Platform. You will learn how our system deals with files, how it helps you organise and manage your data and how to share data with your colleagues. You will see how easy it is...

Genestack @ Festival of Genomics

Blog
Two weeks from now Festival of Genomics is coming to Excel London Exhibition Centre. We wouldn't miss it! You can explore the speakers list here. We hope to see you all there. Make sure to visit our booth! See you soon, Genestack team &nbs...

Platform Update 0.26.0 – What’s New

Platform news
Good news! It's time to announce our next release – Platform Update 0.26.0. It comes with several new important features and interface improvements as well as bug fixes and performance enhancements. First of all, we've added a new interface feature:...

Whole-genome bisulfite sequencing data analysis on Genestack platform

Blog
Bisulfite sequencing approaches are currently considered a “gold standard” for detecting DNA methylation. One of them, whole-genome bisulfite sequencing (WGBS), provides single-base resolution of methylated cytosines in genomic DNA. Investigating t...

New Updates to Genestack Platform Allow Easy Scripting Access

Press releases
For immediate release 23 November 2015 New Updates to Genestack Platform Allow Easy Scripting Access New Python Client Library for programmatic access and for uploading of third-party applications to the platform. Cambridge, 23 November 2015 … Genesta...

Genestack Launches New ‘Expert Series’ of Video Tutorials

Press releases
For immediate release 19 November 2015 Genestack Launches New ‘Expert Series’ of Video Tutorials Tutorials will show users how to gain the most from Genestack’s bioinformatics platform Cambridge, 19 November 2015 … Genestack, the developer of a next g...

Platform Update 0.25.0 – What’s New

Platform news
In this release - Platform Update 0.25.0 - we'd like to introduce a new public data flow - Targeted Sequencing Quality Control. This data flow will allow you to create reports containing both exome and target enrichment statistics. Moreover, Genestack's M...

New raw sequencing data quality control tool available on Genestack

Platform news
We’re excited to announce that we launched a new app: FastQC Report.It performs quality control checks on raw sequencing data and generates a bunch of QC reports telling you in which areas there may be problems. These reports cover the following: b...

Testing differential gene expression on Genestack platform

Blog
One of the most widespread applications of RNA-seq technology is differential gene expression (DGE) analysis. By understanding how gene expression levels change across different experimental conditions, we can gain clues about gene function and learn how ...

Platform Update 0.24.0 – What's New

Platform news
We are excited to announce our next release - Platform Update 0.24.0! Even though this release isn't a huge update with new platform apps, it does contain a new Welcome Page feature, bug fixes as well as performance improvements. First of all, we ad...

Genestack Awarded Grant for Agri-Genomics Collaboration With Rothamsted

In the media
Genestack Awarded Grant for Agri-Genomics Collaboration With Rothamsted
Genestack announced today that it has received a £90,000 ($138,300) grant from Innovate UK to collaborate with Rothamsted Research on the development of agri-genomic technologies for crop improvement. The partners will initially collaborate on a feasib...

Genestack Secures Innovate UK Grant

Press releases
For immediate release 12 October 2015 Genestack Secures Innovate UK Grant New grant will see Genestack expand its capabilities into agri-genomics Cambridge, 12 October 2015 … Genestack, the developer of a next generation enterprise platform for genomi...

New dashboard-style start screen for Genestack

Platform news
We are very proud to announce our Welcome Page: a new Genestack start screen application! We think this dashboard-like app will make it easier for you to work on the platform. From this app you can manage and search data, setup and launch analysis ...

Platform Release 22.09.15 – What's New

Platform news
We are excited to announce our new release: several new apps and a lot of improvements! First of all, Genestack launched new FastQC Report app, which performs quality control checks on raw sequencing data and generates several QC reports telling yo...

Meet our new PR/Marketing intern!

Blog
Hi everyone! My name is Kalina and I have recently joined Genestack as a PR/Marketing Intern. A few months ago I graduated from UCL with a Masters in Human Genetics. During the last couple of years I worked in various labs: some academic, researching ag...

Indexing the World's Public Sequencing Data on Genestack

Blog
Hi! My name is Michal and I'm currently studying Mathematics and Computer Science at the University of Oxford. I have just finished the second year of my degree and joined Genestack for a summer internship. I'm currently developing a Genestack applicatio...

Transcriptome assembly from RNA-seq data

Blog
Hi! I’m Richard, I’m currently two years into a maths degree at Cambridge University and am spending the summer as an intern at Genestack.  I’m currently working on building and evaluating pipelines for transcriptome assembly from RNA-seq data in partn...

WGS Reports for Human iPS Cell Lines

Blog
Hi Everyone! I’m Naomi and I’ve joined the Genestack team as a summer intern during my PhD in Genetics at the University of Cambridge. I’m currently working on developing an application to generate an informative, easy-to-read, visual report for genomi...

Navigation in Genestack Genome Browser

Blog
We constantly strive to improve Genestack's Genome Browser, making it more convenient and intuitive for our users. In the previous update we presented ways to work with multiple tracks at once. Today we’ll demonstrate our track navigation features, which ...

How to import and organize genomic data in the cloud

Blog
Genestack platform allows its users to upload large datasets to the cloud and keep them organized and format-free. In this guide, we'll import data from Merkin et al. 2012 experiment and show how Genestack makes this process fast and reliable. Step 1: ...

New Projects for Pistoia

In the media
New Projects for Pistoia
Alongside updates on current projects, the audience heard three use-cases from organisations that have deployed Pistoia Alliance outputs to good effect. Daniel Baeschlin of Novartis presented their adoption of a CSCS solution, Stefan Klostermann of Roche ...

Four new apps & detailed app descriptions

Platform news
New release includes apps for work with Mapped Reads and Genomic Variations, detailed descriptions for Preprocess and Analyse apps, as well as performance enhancements and bug fixes. Merge Mapped Reads Imagine you’d like to merge several Mapped Reads ...

File organization on Genestack platform

Platform news
You can have dozens of files, folders and experiments used for different purposes and without a good file system, all of them would be just one large body of information with no way to tell you where your important data is located. But! With Genestack Fi...

Testing Differential Isoform Expression on Genestack Platform

Blog
Detecting differential isoform expression from RNA-seq data is one of the common transcriptome analysis tasks. And the purpose of this tutorial is to show you how to perform this analysis on Genestack platform. You know that in the process of alternative...

New platform release! Improved file import, metainfo editing and much more!

Platform news
Today we are happy to announce our next release which brings a range of new features as well as bug fixes and performance improvements. Improved Command Line App Interface First of all, based on your feedback, we've updated the command line apps int...

Bioinformatics: Year One

Blog
It’s been one year since I joined Genestack: I can safely say that it’s been the quickest year of my life! Last February I was welcomed by a brilliant and ambitious team who had managed to build a competitive cloud-based Bioinformatics platform in litt...

Editing Multiple Tracks in Genome Browser

Blog
In our previous post about our Genome Browser we showed how to prepare your view for further analysis using new  track customization features, computing a formula or overlaying individual tracks onto a single one. Some users have found it a little bit...

Interactive Sequencing Quality Control Reports

Platform news
We've just released a new application on Genestack: the Multiple QC Report! It allows you to integrate the analysis of multiple quality control reports on large-scale datasets by producing an interactive graph combining data from individual assay r...

Doing Mathematics in the Genome Browser: Graphs and Formulas

Blog
Genestack Genome Browser is designed to make it comfortable for you to work with your data. We added the ability to customise graph tracks this week, to prepare your view for further analysis or for sharing it with your colleagues. Don't overlook the quit...

Using Genestack for pharmacogenomics research

Blog
My name is Roma Kurilov, I study in Heidelberg at the Helmholtz International Graduate School for Cancer Research at the German Cancer Research Center (DKFZ). I have always been interested in molecular biology: since doing my bachelor’s degree I have wo...

Bioinformatics reproducibility and why it matters

Blog
Guest post: Dr. Jelena Aleksic is a computational biologist at the Stem Cell Institute at Cambridge University. She works on the role of RNA methylation in neurodevelopmental disease. When it comes to my profession, there are certain things that keep m...

Genestack at Genome Informatics 2014

Blog
Genestack at Genome Informatics 2014
Genestack sponsored Genome Informatics 2014 (GI2014), a four days conference held at Churchill College, in Cambridge. We were very excited to attend such an established event, and for many of us this 14th edition was the first. Needless to say, our ex...

Single-cell RNA-seq analysis tutorial

Blog
Single-cell RNA-seq is a recent, exciting upgrade of high-throughput transcriptomics technology, allowing sequencing the RNA of individual cells, allowing investigating transcriptomic heterogeneity within cell populations. This is of particular interest i...

Genestack’s Genome Browser update

Platform news
Genestack’s Genome Browser update
Genestack Genome Browser just got updated! Our free browser keeps growing, allowing Genestack users to share and discuss their data tracks and browser pages in an intuitive and reproducible way. The latest release of Genestack Genome Browser comes with tw...

Genestack at DNA Techonology Symposium

Blog
Genestack at DNA Techonology Symposium
Genestack attended Illumina’s DNA Technology Symposium, a celebration for reaching the “1000 dollar genome” milestone. The event was kicked off by Prof. Shankar Balasubramanian, co-founder of Solexa, whose collaboration with David Klenerman led to the dis...

Attention Developers! We're hiring :)

Blog
We're looking for software developers in Cambridge and in Russia. Help write new bioinformatics apps, and build user interfaces and data visualisations! See our Careers page.

Our First Internal Hackweek

Blog
Our First Internal Hackweek
Last month we ran our first hackweek! We think it was a success and we want to share with you our experience. We also expect that before too long we will be able to share with you some of its outcomes. In this blog post we describe how our hackweek went. ...

Meet Genestack’s Summer Interns!

Blog
Meet Genestack’s Summer Interns!
Hi ! I’m Daniel. I joined Genestack as an intern, to help in the development of software dedicated to the analysis of single-cell RNA-seq data. I come initially from an engineering background, and during my degree, I had the opportunity to work on thr...

4 New Things in Genestack.org

Platform news
4 New Things in Genestack.org
Last Friday, April 18 we updated the Genestack Platform. Here’s what’s new: New look for the applications menu in File Manager The four rubrics are colour-coded and correspond to application icon colours now. If you develop an application for the pla...

Genestack’s Key Ideas

Blog
Chatting on Facebook, a friend asked to explain a bit about Genestack Platform, how it was different from Galaxy. So, here’s the response. Here are some Key Ideas about Genestack Platform, just to grab a few. First Key Idea is that we’re format-free. Y...

Methylation Profiling Using Genestack Platform

Blog
Whole-Genome Bisulfite Sequencing (WGBS) is a powerful approach for genome-wide analysis of the methylome at single-base resolution. DNA samples undergo bisulphite treatment, leading to the conversion of unmethylated cytosines into uracils. Methylated cyt...

Variant Calling Using Genestack Platform

Blog
Single nucleotide polymorphisms (SNPs), together with insertions and deletions (indels) represent almost all human genetic variations. Studies on these mutations focus on the identification of genomic markers for monogenic and complex diseases, such as di...

New Industry Emerging to Provide Cloud-based Computing Firepower Needed for Big Data Genomic Analyses of Healthcare and Medical Laboratory Information

In the media
New Industry Emerging to Provide Cloud-based Computing Firepower Needed for Big Data Genomic Analyses of Healthcare and Medical Laboratory Information
Cloud-based genetic research networks that facilitate collaboration by stakeholders worldwide may solve the most difficult disease challenges, including a cure for cancer Read the full article on how cloud computing could help solving medicine's greate...

The EC2 Spot Instance Life Cycle

Blog
Managing Spot Instances Genestack Platform runs on various commodity compute clusters, from large-scale cloud providers like Amazon, to custom-built systems like IBM’s GPFS + LSF combination. When we use Amazon’s EC2 for internal development, ...

Presenting Genestack Platform at GSC 16 in Oxford

Blog
We are giving a quick presentation of Genestack's capabilities for managing and sharing genomics data and tools at the 16th Genomic Standards Consortium Meeting in Oxford, UK on 1st April at 15:10.

Technology Workshop at Oxford NGS 2014

Blog
Next month we are running a workshop in Oxford at the 2nd Oxford Next Generation Sequencing event,Oxford NGS 2014. The conference runs from 31 March until 3 April 2014; ours is the first workshop, at 16:00 on 2 April 2014. We are excited to introduce Gene...

Genestack Platform Workshop at Oxford NGS 2014

Blog
Next month we are running a workshop in Oxford at the 2nd Oxford Next Generation Sequencing event, Oxford NGS 2014. The conference runs from 31 March until 3 April 2014; ours is the first workshop, at 14:00 on 2 April 2014.

Introducing Genestack’s Bioinformatics team

Blog
Hello, I am Maria! I joined the Genestack team to help creating applications for biological data processing. I have studied molecular biology at Saint-Petersburg State University in Russia and my background is mainly experimental. Today’s technology ...

Alessandro Riccombeni joins Genestack

Blog
Hi, I am Alessandro, and I just joined Genestack to help with the development of bioinformatic applications. I started doing research at the bench, and trading my pipette for UNIX let me enjoy bioinformatics from the point of view of an experimental bi...

2013 Sequencing and Bioinformatics in the Rear View

In the media
2013 Sequencing and Bioinformatics in the Rear View
Now is a good time to reflect on the last year of DNA sequencing and bioinformatics industry gyrations. Besides, we're already 1/12 through the year, so one had better reflect quickly before last year and this year blend together. Read the full article...

Open Source LSF Java Client

Platform news
We’ve been working with folks from IBM on enabling Genestack Platform to use LSF as its grid engine. To do this, we needed to communicate with LSF from Java. It turns out there’s no easy way to achieve this, and so we wrote a simple Java client library...

July Alpha Release

Platform news
July Alpha Release
Last month we rolled out an update to the platform, with several important new features. New applications: command line tool integration It is easy to integrate command line based tools, like bowtie, bwa, or custom scripts into Genestack. Command Li...

Alpha Update

Platform news
Alpha Update
We are rolling out an update to the Genestack Platform Alpha In addition to various bug fixes, the following is new in this release: Feedback: you can now send us messages using the feedback button near the bottom-right corner of the screen!   ...

Bio-IT World 2013

Blog
Bio-IT World 2013
We had a great three days in Boston at Bio-IT World 2013! Some remarkable presentations, and new products. Coinciding with Bio-IT World, we are proud to announce that now anyone can sign up to test Genestack Platform . Just go to https://genestack.com/...

Going to Bio-IT World 2013

Blog
Our CEO Misha Kapushesky is presenting Genestack Platform at Bio-IT World on Wednesday, April 10. See you in Boston!

Genestack Platform Alpha

Platform news
Genestack Platform Alpha
We are kicking off the alpha of our new platform for building bioinformatics applications! We at Genestack are dedicated to making the life of a bioinformatician, whether embedded in a hospital, running the bioinformatics for a biotech, working in a co...

Amazon Takes Genomics Research to the Clouds

In the media
Amazon Takes Genomics Research to the Clouds
“The genomics revolution people talked about 10 years ago? It is happening now,” Misha Kapushesky, CEO of genomics startup Genestack, tells Wired. “This is just the tip of the iceberg.” Read the article

Misha Kapushesky presents at Bio-IT World 2012

In the media
Misha Kapushesky presents at Bio-IT World 2012
Presenting in the Cloud Computing track as a Featured Speaker, Dr. Kapushesky, Genestack CEO, introduces a preview of the Genestack Genomics Applications Platform. Slides from the presentation are available on SlideShare.

Genestack & Pistoia Alliance Sequence Services Phase 2 RFP

Blog
Pistoia Alliance, a not-for-profit consortium of pharmaceutical companies, launched the Sequence Services Phase 2 project, seeking a platform for analyzing and storing next-generation sequencing (NGS) data. We were selected from more than 10 submitted pro...

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