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On wrote:

GeneProf v2

On Tuesday, we have made the first public release of GeneProf 2.x available to the public. This is a major re-work of the GeneProf core engine, although you might find that it looks remarkably similar! Most changes have happened on the back-end and users will generally not directly notice most of them. However, in the coming months we'll be rolling out several new features made possible by the deployment of v2, so keep an eye on the updates! Here's an (incomplete) list of some new features in GeneProf v2: * Modernised and improved web site, which should provide better accessibility and responsiveness. * Quick-access functions, e.g. to directly access experiment workflows from the main page or experiments browser page. * Major overhaul of the database backend enabling distributed and more scalable storage of huge experimental datasets. * It is now also possible to copy datasets over TO other experiments (rather than copying them FROM other experiments). * Tweaks to analysis wizards to make them even easier to use. * Improved user guidance on analysis module configuration pages. * Sleek login page benefiting from the Stembio User Account SSO (Single Sign On) system. * URL-based data imports are now executed on the processing servers, so you no longer need to wait in front of your browser until they're finished. * T-test calculator: We've added a simple calculated for two-sample t-tests in addition to the popular hypergeometric test calculator. * Many bug-fixes. Like any new release, GeneProf v2 is likely to have a few minor bugs that have escaped our attention. If you notice any problems, please report them via the bug-tracker tool!
On wrote:

Upcoming maintenance

Due to an upcoming maintenance operation, GeneProf will stop processing new analysis jobs on Friday, the 5th of December (approximately noon time). This outage is expected to last for about a week. We will provide you with updates in due course and apologise in advance for any inconvenience caused! The GeneProf server (for data browsing) will remain accessible for the majority of the maintenance period.
On wrote:

200 and counting!

GeneProf team member AK has just released another experiment to the public GeneProf databases, brining the count of public experiments to 200! The experiment comprises several dozens of ChIP-seq datasets from the ENCODE project, adding further to the pool of epigenome data in the system. GeneProf's growing fast and more experiments will come out in the future. We're also happy to report that a number of users have started contributing to the database, doing their bit in making genomics data more easily accessible to the scientific community. If you'd like to contribute, it's easy to get started: Just sign up for an account and start analysing your own or data from public repositories right away. Public data does not count towards your quota and we're always happy to make special allowances for people that help to feed data into the system.
On wrote:

Downloads

We have now updated the downloads of the GeneProf software for local installation in academic institutions to the latest version of the tool (version 1.1403124). Downloads are available to registered users after accepting the user license.
On wrote:

GeneProf's back!

Good news, everyone! GeneProf's main web presence is now back up running after an temporary downtime caused by some hardware faults. All public components of the GeneProf website have been fully restored and the remainder of the system will be back soon. We'll provide further details after all services have returned!
On wrote:

NAR Databases 2014

The 2014 NAR Database Issue has been published a couple of weeks ago, containing the latest GeneProf paper: Full article: http://nar.oxfordjournals.org/content/42/D1/D851
On wrote:

Happy New Year!

Seasonal greetings and best wishes for 2014 from the GeneProf team!
On wrote:

BioServices meet GeneProf

Thomas Cokelaer over at the EBI has integrated GeneProf's web services into his BioServices tool. BioServices is a Python package that makes it incredibly easy to use various bioinformatics web resources (apart from GeneProf it supports, for example, EUtils, KEGG, PDB or PathwayCommons). You can read more about BioServices and GeneProf in the web services documentation or directly on the BioServices website.
On wrote:

New Server

The GeneProf web application has moved to a new server with massively improved hardware. We would expect that you will notice significant speed improvements! There will be further speed improvements with a further hardware upgrade in the next few weeks.
On wrote:

GeneProf Data Paper

We're delighted to announce that Nucleic Acids Research has just released an advance access version of the latest GeneProf paper. In this article, we describe GeneProf as a data resource and illustrate how it may be useful for researcher seeking instant access to high-throughput genomics experiments. The full reference to the paper is: GeneProf data: a resource of curated, integrated and reusable high-throughput genomics experiments Florian Halbritter; Anastasia I. Kousa; Simon R. Tomlinson Nucleic Acids Research 2013; doi: 10.1093/nar/gkt966 And here's a link to the full text version of the paper at NAR.
On wrote:

Hardware Upgrades

We're in the process of upgrading some of the hardware that GeneProf is based on. Unfortunately, this will mean that GeneProf will be intermittently unavailable over the next few weeks, but on the plus side you should notice some performance improvements in the long run! We'll try to minimise downtimes and will announce any server shutdown in advance whenever possible so to avoid causing you any more inconvenience than strictly necessary. Please let us know if you experience any problems.
On wrote:

More Video Tutorials

We have recorded a collection of new video tutorials covering several aspects of the GeneProf interface. The full list of videos is available here, or alternatively all videos have been uploaded to this YouTube playlist.
On wrote:

Data Galore

A few days ago we've started rolling out a number of new datasets to the public GeneProf databases including some large data collections from the ENCODE project. We realise it's been a bit quiet over the previous month, but we've been working on a lot of projects and many of these are now ready to go public -- so watch this space, there's a whole lot of data to come! As usual, if there's a particular dataset you'd like to see included in GeneProf either consider adding it yourself or request it to be added (requirs login!).
On wrote:

GeneProf Powers iPS Research

The Kaji lab at the Centre for Regenerative Medicine (University of Edinburgh) have published exciting new research tracing the routes leading to induced pluripotent stem (iPS) cells. Spearheaded by James O'Malley, the team followed the reprogramming of fibroblasts and, using a combination of novel markers, characterised a series of defined stages in the process. The researchers profiled the global gene expression in cells from all these stages using a multiplexed RNA-seq strategy and used GeneProf to analyse the data generated, identifying groups of mechanistic genes with distinct expression patterns. Read up the details in the original research publication: O'Malley J, Skylaki S, Iwabuchi KA, Chantzoura E, Ruetz T, Johnsson A, Tomlinson SR, Linnarsson S and Kaji K. High resolution analysis with novel cell-surface markers identifies routes to iPS cells. Nature, 2013, doi: 10.1038/nature12243. PMID: 23728301
On wrote:

New Paper

Another paper making use of GeneProf for the integration of gene expression data (from microarrays) with public ChIP-seq data has just been published in Cell Stem Cell. Karwacki-Neisius and colleagues have investigated the effect of altered levels of the stem cell core regulatory Pou5f1 (also known as Oct4) on pluripotency and self-renewal in mouse embryonic stem cells. Here's the reference to the full research paper: Karwacki-Neisius V, et al. Reduced Oct4 Expression Directs a Robust Pluripotent State with Distinct Signaling Activity and Increased Enhancer Occupancy by Oct4 and Nanog. Cell Stem Cell (2013). PMID: 23642364. And this is the GeneProf experiment with the related data analysis: gpXP_001177.
On wrote:

New Workflow Designer

With today's new release of GeneProf (v1.13013) we have launched a new version of the workflow designer tool. The new workflow designer should be a lot faster to load (especially for very large workflows), look smoother and more comprehensible and be overall a bit more straightforward to use. Please don't hesitate to let us know your thoughts and please report any issues you might find with the new tool. For those interested in the technical details: We have used the great jsPlumb JavaScript library (http://jsplumb.org) to implement the new workflow designer. The library wires is tightly integrated with jQuery (but also works with MooTools and YUI) and works like a dream -- highly recommended!
On wrote:

Paired-end FASTQ

The new version of GeneProf (launched today) brings better support for paired-end FASTQ files via the data analysis wizards: Previously, there had been no convenient way from within the data analysis wizards to use datasets with more than one input data file for the same dataset. The new version of GeneProf (v1.130123) add advanced configuration options to the RNA-seq and ChIP-seq wizards that overcome this issue. Instead of simply providing one drop-down menu for the file format of each input file, you can now open up a new dialog box with different configuration options, including one for paired-end FASTQ files! We're keen to hear feedback and suggestions about the new config dialogs, so please don't hesitate to get in touch!
On wrote:

Genome Browser fixed

After last week's update you might have noticed that the genome browser blots would not update after changing the selection of tracks. This was due to an attempt to make better use of browser caching of previously rendered genome browser images -- unfortunately with unforeseen consequences. This issue should now be fixed and the genome browser ought to be fully functional again!
On wrote:

GeneProf Web Services

GeneProf now provides a collection of web services that allow programmatic retrieval of data from its databases! A list of all web services alongside many illustrative examples (in Perl, Java, R, Taverna, Galaxy and more) is available from the new web services homepage. We're keen to hear your feedback on the new web services, so please don't hesitate to get in touch!
On wrote:

First GeneProf-powered Paper

Festuccia et al. have just published the first paper benefiting from GeneProf-powered analysis in the latest issue of Cell Stem Cell. The paper investigates the downstream targets of the transcription factor Nanog, a key regulator of embryonic stem cells, and highlights Esrrb as one of the most prominent targets. GeneProf has been used to analyse DeepSAGE sequencing data from a variety of mouse cell lines and to combine these data with microarray and ChIP-seq data. Details about the analysis are available in the GeneProf experiment (gpXP_000385) and the full reference to the paper is: Festuccia et al., Esrrb Is a Direct Nanog Target Gene that Can Substitute for Nanog Function in Pluripotent Cells. Cell Stem Cell, 2012.
On wrote:

Correlated Genes

There's now a new section in the gene summary pages highlighting genes with similar expression patterns to the gene of interest. The correlation values are Pearson correlation coefficients calculated on the basis of all public gene expression data in the GeneProf systems. Since this calculation depends on the availability of a sufficient amount of data, the "correlated genes" section will only be included in the summary page for organisms for which there is enough data available.
On wrote:

Power Maintenance

We have just received notice that there will be a scheduled power cut in the building hosting the GeneProf servers in order to perform some critical maintenance work on 16/August/2012. As a result of this, the GeneProf servers might be temporarily unavailable from about 10am to 1pm on this day. Please accept our sincere apologies for any inconvenience caused.
On wrote:

Recent Updates

We have implemented a few minor changes and bugfixes over the last weeks. The most important changes are: * New Feature: Password-based sharing of experiments. If you plan to publish a paper benefiting from GeneProf analysis, you can now share your experiment prior to making it public with reviewers by generating a password token which you can pass on to others. From your experiment's main page select "Add/Remove Collaborators.." for data sharing. * Fixed a number of bugs that caused data imports from the SRA and ENA not to work. GeneProf had been unable to interpret some of the metadata retrieved from these sources. * Improved "Import Data from other Experiments" interface. The dialog boxes have been updated in a way that makes it easier to locate important data in other experiments. * Lots of minor bugfixes and improvements...
On wrote:

Recent GeneProf Updates

We've launched a number of changes and improvements to the GeneProf interface and backend over the past weeks. Here's a list of the most noteworthy updates: * Wizards: The RNA-seq and ChIP-seq wizards have been updated. The new versions of the wizards make it possible to more easily define sample groups on the basis of arbitrary sample annotations. The ChIP-seq wizard now produces an additional output dataset in which individual ChIP-seq peaks from multiple datasets have been merged, making it possible to quickly filter results to identify overlapping binding regions. * Cookies policy documents: In compliance with the new regulations about the use of "cookies" in web pages, we have added a page explaining how we use cookies in the GeneProf web app. * Uploader: We've fixed a number of bugs that people have been experiencing with the GeneProf uploader tool. There are a few minor issues outstanding, but we hope to fix those within the next weeks. * New modules: A number of new modules have been added for the creation and manipulation of reference datasets (creation of transcriptome-only references, creation of references from GenBank records, extraction of genomic data from references). We have also added a new module to quantify the number of aligned reads in arbitrary genomic intervals. Several further modules are currently being tested, so stay tuned for more! * Minor interface improvements: Many minor improvements to the interface have been made -- hopefully this will make for a more pleasant user experience!
On wrote:

Server Problems

Frequent GeneProf users might recently have found that the service was temporarily unavailable for a few hours. We are sincerely sorry for any inconvenience this might have caused -- and we're working hard trying to figure out the cause of these instabilities! Details to follow as we find out more!
On wrote:

Power Upgrade

The GeneProf servers will be unavailable on Thursday, 16 Feb 1012, from approximately 17:00-18:00 (GMT). This is due to a power upgrade being installed in the server room and work is meant to be completed within one hour. In preparation for the shutdown, GeneProf processing nodes will be gradually taken down starting from 4pm, the web server will remain in operation until immediately before the upgrade.
On wrote:

New Release

The latest GeneProf release (1.120125) has just been released to the public server. The new version features slightly improved plots for all automated summary reports, an extended manual (with the section on custom references filled in) and a few minor tweaks.
On wrote:

Rice and Arabidopsis

We have now added an additional reference dataset for rice (O. sativa; as by feature request http://www.geneprof.org/show_issue.jsp?id=15). Also, we were temporarily forced to retract the A. thaliana reference dataset after we had noticed minor faults in the data, but have now re-added the reference dataset. Both datasets are based on the latest genomic annotations from Ensembl Plants 12 and the latest genome assemblies (TAIR10 for A. thaliana and MUS6 for rice).
On wrote:

GeneProf Release

We're delighted to report that the GeneProf paper has just been published in the latest issue of Nature Methods: Halbritter, F., Vaidya, H.J. & Tomlinson, S.R. GeneProf: analysis of high-throughput sequencing experiments. Nature Methods 9, 7รข??8 (2012). http://www.nature.com/nmeth/journal/v9/n1/full/nmeth.1809.html Accordingly, GeneProf has now officially been released to the public. We hope you'll find it useful for your research. Please do not hesitate to get in touch about suggestions, ideas, problems or whatever else you might have on your mind!
On wrote:

We're moving!

The Institute for Stem Cell Research is moving to its new home at the SCRM building across town.. and so are the GeneProf servers. As a consequence, we expect downtimes during the next days and we needed to temporarily take all processing nodes offline. This means you will currently not be able to run any analysis jobs in GeneProf. We hope all systems will be back to normal by the end of next week (25 Novemeber 2011) the latest and do apologize for any inconvenience caused!
On wrote:

GeneProf's back!

We've completed the essential system maintenance over the past weekend and all GeneProf services should now be back to normal. As a part of the maintenance work, we've also deployed a new version of the GeneProf web application and made quite a few changes to the interface. If you happen to notice any problems, please report them via the bug tracking tool ('About & Help' > 'Report Bugs & Features'). Thanks!
On wrote:

System Maintenance

The GeneProf systems will be undergoing some essential maintenance starting Friday, 9 September. Some services will be temporarily unavailable. This includes all processing nodes, i.e. it will not be possible to run any new experiments for a while. We expect all services to return by Monday (September 12). We apologize sincerely for any inconvenience caused.
On wrote:

API, Modules & Manual

GeneProf now offers a new feature: Computer programmers and IT experts can access a large part of the public GeneProf data via a special new Web API. We've also added some documentation about how to go up developing new GeneProf workflow components. Check out the manual which has been updated to reflect the most recent changes. For the new API features, check the 'Advanced Topics' chapter!
On wrote:

New Update Policy

We've recently restarted the GeneProf servers quite a few times. Realizing that this might be quite disruptive of your work, we'd like to apologize to all test users. In future, all regular updates to the GeneProf system will be rolled out during a weekly mainenance session on Wednesday mornings (UK time). Only in exceptional cases, it might be necessary to restart the service in order to implement urgend bug-fixes or resolve other issues essential for the save running of the GeneProf web services. Thanks!
On wrote:

Better Interface, Collaborations & Data

Over the last month or so, we've made further improvements to the GeneProf web interface, notably further improving the built-in genome browser. The track configuration now contains further customization options: - Plot type: Choose between GeneProf's original line-style coverage plots and more traditional bar/area type of charts (as known from UCSC, Ensembl and the like). - Axis scaling: You know have additional options to define the axis scaling (both, in terms of range and between-library normalization). - Label position: Some users prefer track labels to appear below the browser tracks. You can now specify the relative position of labels in the options dialog (or turn them off completely). There are also additional navigation buttons to more quickly zoom in / out of the current region and move left or right. New feature: Collaborations: It is now possible to share on-going data analysis experiments with collaborators. This should hopefully help to facilitate effective collaborations across international projects by elmininating the need to constantly transfer data and preliminary results between different locations. To use the feature, have a look at the "Things you might like to do.." section of one of your own experiments -- you'll be able to search for other registered GeneProf users and to add them as a "collaborator" to your experiment. Lastly, we've added lots more data to the public GeneProf databases. GeneProf now stores over 8 billion short read sequences along with all readily interpretable results and visualizations.. Check out what's new by clicking here.
On wrote:

Improved Genome Browser

We've worked on the GeneProf's genome browser and made some improvements. The new version should be a little, but notably faster thanks to advanced data retrieval methods. We've also added a whole load of new features: - Improved track selection: With the amount of public browser tracks constantly increasing, it was getting more and more difficult to find the tracks you were looking for -- luckily, you can now search, filter and sort tracks to make this a little bit easier! - Change the order and colour of tracks! Add tracks in the desired order to influence the layout of the browser graphics and choose from a range of pre-defined colours or choose one yourself. - You can now jump between multiple active browser sessions, continue previous sessions after navigating away from the page and you can even persist (permanently store) browser sessions and reload them at a later point in time.
On wrote:

Screencasts!

We have added some screencasts (short videos) illustrating some of the most popular and interesting features of GeneProf. All videos can be found in the screencasts section.
On wrote:

Manual Complete

We've just completed the first version of the GeneProf documentation. There are still some bits that we want to elaborate on, but it's already pretty comprehensive! If you find something that's missing or unclear, please don't hesitate to get in touch!
On wrote:

Closed Beta Open!

GeneProf has now been deployed at its final web server (http://www.geneprof.org). Access is currently restricted to a number of selected test users.