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Data Discovery Portal and Confluence Maintenance

 

Dear Users,

We will be updating the Data Discovery Portal to align with the latest main programme data release v13. The application will be unavailable 09:00-14:00 21st October, while we complete the update.

There will also be a short outage of Confluence, which hosts the RE help pages, 20:00-22:00 14th October.

We apologise if this causes any disruption to your work.

Best wishes,

Genomics England

Participant Explorer Update

 

Dear Users,

We will be updating the Participant Explorer with the following new features:

  • Compare multiple participants: view the combined medical history timeline of up to 12 participants 
  • Group clinical codes on the timeline based on subsumption 

The application will be temporarily unavailable during the update, the estimated outage will be 9:00-12:00 Thursday 14th October. For more information about the Participant Explorer, please see the Help documentation at https://research-help.genomicsengland.co.uk/display/GERE/Participant+Explorer


We apologise if this interrupts your work at all.

Best wishes,
Genomics England

HPC Helix disruption: 7th-14th September

 

Dear Users,

We would like to make you aware of an upcoming disruption in HPC Helix for 7 days between the 7th and 14th September, during which jobs are expected to remain in a pending state for a longer time.

The reason for this is to complete internal collaborative work regarding the phasing of aggV2. A substantial number of nodes will be reserved (30/50n) within this period. After this, the reservation will be reduced to a lower impact (5/50n) for another couple of days, after which the reservation will be removed, and we expect your jobs to return to normal. Please bear in mind that all jobs that have been paused or pending will start again, so there may still be some delays after the reservation period.

You can still submit jobs as per usual during this period, but this is an advanced notice that they may be in the queue for a longer period or that they may become suspended for a certain amount of time.

Finally, we will need to start draining jobs from the nodes reserved for the upcoming phasing work. Therefore, jobs submitted to the long queue one week before the reservation period and jobs submitted to other queues 24 hours before the reservation period will experience more pending states. We want to emphasise that users can submit long jobs during the draining phase, but these will not be dispatched until at least the 7th of September.

We apologise for any impact on your work, but we aim to share these valuable data with the research community at a later stage.

Best wishes,

Genomics England

Airlock Update - 16:00-18:00 26th August

 

Dear Users,

The Airlock system (Manage File Transfer) will be temporarily unavailable, 16:00-18:00 26th August, while it is updated.

Please ensure you submit your export requests outside of this maintenance window.

Best wishes,

Genomics England

Clinical Collaboration Requests Used in Publications

 

Dear Research Community, 

As you are hopefully aware, if you identify a potential new genetic diagnosis or a variant of interest about which you would like to contact the recruiting clinician, you can fill in the Researcher-Identified Potential Diagnoses and Clinical Collaboration Request Forms available as part of the Airlock. Please see the FAQs for researchers at the clinical-research interface for more information about these processes.

We have had over 500 clinical collaboration requests submitted so far this year, and we know some of the collaborations have led to papers being published.

We would love to hear about more clinical collaboration success stories. If you have been involved in the publication or submission of a paper which involved information from a clinical collaboration request (CCR), please let us know by clicking 'Yes' below. We may then email you to ask for more information.

Thank you for your help,

Genomics England

Upcoming maintenance: Airlock and Data Discovery Portal

 

Dear Users,

Please be aware of the following scheduled updates for the Airlock and Data Discovery Portal, both of which will be unavailable during the maintenance window. Please plan your work around these scheduled outages.

  • Airlock update: 16:00-18:00, 4th August
  • Data Discovery Portal update: 09:00-10:00, 5th August

Best wishes,

Genomics England

Version roll back of R application

 

Dear Users,

As part of our previous maintenance cycle, we recently upgraded the default R within the Research Environment to v4.1.0. We have subsequently found an incompatibility between this version and the ggplot package which is affecting several users.

To resolve this matter, we will need to roll back the default version of R to the previous stable version (v4.0.3). We will be performing this change as a priority fix. As a result, there is likely to be a suspension of the availability of the default version of R and RStudio within the Research Environment between 9:30-10:30am 28th July, while we complete this task. Access to R and Rstudio via the module load command will be unaffected.

We thank you for bringing the issue to our attention, and your patience and understanding during this process.

Best wishes,

Genomics England

Research Environment Upgrade - 7.00-9.30am 16th July

 

Dear Users,

We are upgrading the Research Environment from Inuvika v2.8.2.1 to v3.0.1, 7.00-9.30am Friday 16th July, during which time the Research Environment will be unavailable. We have tried our best to select a time that will minimally impact our users, but please ensure that you save all your work before this because all open sessions will be terminated.

Best wishes,

Genomics England

Automatic log out after 48 hours of inactivity

 

Dear Researcher,

Thanks to those of you who responded to our proposal to log you off after 24 hours of inactivity, so that we can try to improve stability of the RE. We took your feedback into account and decided to extend this to 48 hours (we hoped to be able to do 72 hours, i.e. over a weekend, but this was not possible). So, from this week onwards, if you do not use the RE for more 48 hours, whether you close the browser or leave it open, you will be logged out. This means that any unsaved work will be lost. So we really strongly suggest that, unless you are sure you will be soon returning, when you leave the RE, you save your work and actually log off using the start menu, rather than just closing the browser. This brings other advantages e.g. no stuck sessions or problems logging in the next time.

I really hope that over the next few weeks you will start to notice real improvements in the stability of the RE.

Very warm wishes,

Anna Need

Product Manager

Airlock back online and upcoming maintenance

 

Dear Users,

Thanks to the efforts of our engineers, the issue with the Manage File Transfer system is resolved and you can now submit your airlock export requests again.

Reminder of scheduled maintenance:

  • Helix will be unavailable from 3pm Friday 2nd July - 5pm Sunday 4th July. Please save your work and log out of interactive sessions on Helix before 3pm today.
  • LabKey and the Research Help pages (Confluence) will be unavailable 7am-9am, Monday 5th July

Best wishes,

Genomics England

Airlock exports unavailable

 

Dear Users,

We have identified an issue where Airlock export requests via the Manage File Transfer system are not working. We are investigating this issue as a matter of urgency and will try to resolve this as quickly as possible. Please refrain from submitting any export requests as you will receive an error message and the request will fail to send.

Apologies for the inconvenience, we will update you as soon as the system is working again.

Best wishes,

Genomics England

RE Labkey and Confluence Outage 7am-9am 05/07/2021

 

Dear Users,

We need to perform some essential maintenance that will mean that LabKey and the Research Help pages (Confluence) will not be available inside the Research Environment. To minimise impact to your work, we have scheduled this maintenance for 7am-9am, Monday 5th July 2021. You will still be able to access the Research Help pages (Confluence) outside of the Research Enviornment using the following URL: research-help.genomicsengland.co.uk.

Best wishes,

Genomics England

Helix Upgrade - Scheduled Downtime 02/07/21 - 04/07/21

 

Dear Users,

From 3pm Friday 2nd July to 5pm Sunday 4th July, Helix will have scheduled downtime for an essential upgrade. Before this maintenance window, please save your work and log out of interactive sessions on Helix. During the window, please do not log into Helix. All queued and running jobs will not be affected.

Best wishes,

Genomics England

Research Environment maintenance - 7am-9am Tuesday 15th June

 

Dear Users,

We are very sorry for the Research Environment outage on 10th June. To prevent this issue reoccurring, we urgently need to increase the memory limit on the servers.

To minimise impact to your work, we have scheduled the maintenance for 7am-9am Tuesday 15th June, during which time the Research Environment will be unavailable. Please ensure that you save all your work before this because all open sessions will be terminated.

We apologise for this short-notice interruption of service, but the sooner we carry out this work, the lower the risk of unexpected outages.

Best wishes,

Genomics England

Important changes to our backup policy

 

Dear Users,

We are making some important changes to our backup policy to optimise data storage in the Research Environment. From 21st June we will no longer be supporting backups older than 3 months on HPC home drives. This will only affect you if you have deleted files more than three months ago and may need that data recovered. If you think this may be the case, please check now and email our Service Desk ([email protected]genomicsengland.co.uk) if you require anything recovered from this time period.

You can read our full backup retention policy for the different Research Environment directories here: https://research-help.genomicsengland.co.uk/display/GERE/Backup+retention+policy

Best wishes,

Genomics England

Participant Explorer v12 update

 

Dear Users,

We will be updating the Participant Explorer with:

  • Data release version 12
  • “Case solved” status and comments from the GMC exit questionnaire table for rare disease participants

The application will be temporarily unavailable during the update, the estimated outage will be 9:00-12:00 Tuesday 8th June. For more information about the Participant Explorer, please see the Help documentation at https://research-help.genomicsengland.co.uk/display/GERE/Participant+Explorer

We apologise if this interrupts your work at all.

Best wishes,

Genomics England

Data Discovery Portal updating to v12 data release

 

Dear Users,

We will be updating the Data Discovery Portal to include the latest v12 data. The application will be temporarily unavailable during the update, the estimated outage will be 9:00-15:00 Tuesday 1st June.

We apologise if this interrupts your work at all.

Best wishes,

Genomics England

Issues with RStudio

 

Dear Users,

As some of you have already reported, we are experiencing issues with Rstudio, R and Rpackages since the upgrade of the Research Environment.

We are currently investigating these together and are working on a stable fix. This may further delay ongoing processes such as software installations or general inquiries. Please continue reporting these issues as they may aid our investigation.

We apologise for the ongoing disruption to your research. We will update you upon any improvements.

Thank you very much for your patience.

Kind regards,

Genomics England

Participant Explorer Unavailable

 

Dear Users,

Due to a technical issue the Participant Explorer is currently unavailable.

We are working hard to resolve this and expect the application will be available again by the end of today.

We apologise for any inconvenience this may be causing.

The Research Environment Squad

Log out after 24 hours

 

Dear RE User,

Due to stability issues caused in part by load of the servers, we are trying to reduce the burden of disconnected sessions. To do this we propose to log out sessions that have been active for more than 24 hours.

We would love to hear your thoughts on this proposed change. Please respond below.

Many thanks,

Anna Need

Product Manager, Research Environment

Research Environment Server Reboot

 

Dear Users,

We have been investigating the stability issues of the Research Environment and as part of our efforts to resolve this, we will need to perform a series of server reboots. In order to minimise disruption to your work, we have scheduled to do these 7am-9am, 7th May. This will mean any open sessions will be automatically terminated, so please can you ensure you save your work beforehand. We aim to have completed the server reboots by 9am, at which point you should be able to resume your work.

Best wishes,

Genomics England

Research Environment Instability

 

Dear RE Users,

We would like to apologise for the instability that you may be experiencing using the Research Environment the last few days (and, unfortunately, ongoing). We are looking into it as a matter of urgency.

Please continue to report issues to the Service Desk as we may be able to help by resetting your session,

Sincerely,

Anna Need and the Research Environment Team

Airlock and Rocketchat scheduled maintenance

 

Dear Users,

Airlock and Rocketchat are scheduled to be upgraded 7:00-10:00am (BST) 28th April. During this time period both applications will be unavailable.

Please schedule any import/export requests or collaborative work around this outage.

Best wishes,

Genomics England.

Decommissioning Inuvika Staging Environment

 

Dear Users,

We are provisionally planning to decommission the Staging Environment due to lack of use. The Airlock system will be unaffected by this change. If you are using the Staging Environment for anything besides the Airlock, please let us know so that we can plan an alternative with you by raising a Service Desk ticket or emailing [email protected].

On 22nd April the Staging Environment will be put into maintenance mode and users will no longer be able to log-in, if there are no objections before 22nd May the service will be decommissioned.

Best wishes,

Genomics England

Participant Explorer "Emergency Care" update
 

Dear Users,

We will be updating the Participant Explorer with a new data set (NHSD Emergency Care) and controls to filter the timeline. The application will be temporarily unavailable during the update, the estimated outage will be 9:00-12:00 Tuesday 13th April. For more information about the Participant Explorer, please see the Help documentation at https://research-help.genomicsengland.co.uk/display/GERE/Participant+Explorer

We apologise if this interrupts your work at all.

Best wishes,
Genomics England

Labkey folder issues

  

Dear Research Environment users,

We are aware that some users are having issues accessing Labkey or specific folders within Labkey.
Genomics England is investigating these issues and trying to resolve this issue as soon as possible.
We apologise for any inconvenience this may have caused and hope to restore full functionality soon.

Best wishes,
Genomics England.

HPC (Helix) Outage: 17:00 - 18:00 24/02/2021

 

Dear Users,


The HPC (Helix) will be undergoing maintenance from 17:00 - 18:00 24/02/2021. To prepare for this we will be making some changes to the HPC queues to minimise the risk of jobs being killed. Please note the following when scheduling your work.


The long queue will be holding all jobs in the queue submitted after 4pm 17th February.
The short, medium and interactive queues will be holding all jobs in the queue submitted after 4pm 23rd February.
All held jobs will resume after 6pm 24th February.


This is to allow a week for all running jobs to finish before the maintenance period. Please avoid submitting any long-running jobs that will not have finished by 24th February. We cannot guarantee that any jobs still running after 4pm on 23rd February will complete successfully. All jobs held in the queues in advance of the maintenance will then be executed as soon as the work is complete. Please ensure you save and exit jobs before the maintenance period.


We apologise for this disruption, if this outage will significantly impact your work or if you have any further queries, please contact our Service Desk: [email protected].


Best wishes,


Genomics England

Participant Explorer v11 data update

 

Dear Users,
 
This Thursday we will be updating the Participant Explorer with the latest v11 data. The application will be temporarily unavailable during the update, the estimated outage will be 9:00-12:00 Thursday 11^th^ February.
 
If you have any problems using this tool after this update please raise a service desk ticket.by going to +https://jiraservicedesk.extge.co.uk/plugins/servlet/desk+ outside of the Research Environment.
We apologise if this interrupts your work at all.
 
Best wishes,
Genomics England

Restart to RE 04/02/2021

 

Dear Research Environment users,

In order to resolve a production issue, we need to restart the Inuvika service in the Research Environment (RE) which will terminate your current RE session, at 8am GMT tomorrow (04/02/2021). To avoid losing any unsaved work, we ask you to save your work and log out before 8am tomorrow. You may log in again shortly after 8.15am GMT.

We are sorry for the inconvenience.

Best wishes,
Genomics England

Data Discovery Portal updating to v11 data release

  

Dear Users,

We will be updating the Data Discovery Portal including the latest v11 data. The application will be temporarily unavailable during the update, the estimated outage will be 9:00-15:00 Thursday 28th January.

We apologise if this interrupts your work at all.

Best wishes,

Genomics England

All Helix Users Need to Set bsub -R & -M Value

 

Dear Users,

As part of stability improvements to LSF queue policies run on Helix, a default memory resource request of 1GB per job is being introduced from 19th January. This is a default setting that will be applied to all jobs unless a user specifies a larger memory request.


What is the Change?

- Change to rusage value required for all job submissions - this will be set at 1GB default value.

- Change to MEMLIMIT value required for all job submissions - this will be automatically set based on rusage value specified by user. For 1GB jobs, MEMLIMIT will be set at 2x rusage. MEMLIMIT will taper towards zero tolerance at 300GB (or above) job submissions.


The changes will be applied to the following queues on Helix:

'short'

'medium'

'long'


What do YOU need to do?

When submitting a job to the short, medium, and long queues on Helix, users need to set rusage values for all jobs needing more than 1GB (1000MB) of memory by adding the bsub option shown here:

'bsub -R "rusage[mem=<desired_memory_in_megabytes>]" '.

Users will have complete ability to change rusage. We advise users to specify a sensible value for rusage for each job, if a job exceeds its memory allocation it will fail.

When a job fails due to exceeding its memory allocation, users will see the following message in their job output: "TERM_MEMLIMIT: job killed after reaching LSF memory usage limit." Users may read more about termination reasons here.


If you have a high memory job:

Please check your job summary to determine the number of processes and threads used by your jobs. For each 8GB of memory needed, users should also request an additional job slot to avoid an imbalance in CPU cores versus RAM. For example, a job using one slot and 280GB memory is highly imbalanced, and the user should request all 34 job slots on a node. Jobs requesting more than 34 slots will additionally need to adjust the span in the resource request.


If you use the 'inter', 'high' and 'pipeline' queues on Helix:

There is currently no default resource requirement enforced on jobs in these queues due to an extended change approvals process. So memory allocation for each job is unknown and uncontrolled by LSF job scheduler.

While the memory allocation change has been temporarily blocked from implementation on these queues, we would encourage users of the 'inter', 'high' and 'pipeline' queues to add rusage and MEMLIMIT values to their jobs as soon as reasonably practical. This will facilitate optimisation of LFS and cluster use among other benefits.

Further details on specifying resource requirements and the runtime memory limit may be found here.


Best wishes,

Genomics England

New COVID data

 

Dear Users,

We are happy to announce that we have released an update of COVID-19 testing data for 100,000 Genomes Project participants representing Dec 2020 data. These can be found in LabKey, in the “Frequent Release” project (at the same level as Main Programme). The data give information on the time of tests, specimen types, laboratories, requesting organisations, positive/negative test results and any dates of death. There are data on 10,617 test results, linked to Participant IDs. A data dictionary for these data can be found https://research-help.genomicsengland.co.uk/display/GERE/Frequent+Data+Release


Best wishes,

Genomics England

Participant Explorer Update

 

Dear Research Environment users,

The Participant Explorer will be taken offline on Tuesday 8th between 9am and 3pm to install an update to the system. 
This update will add a file path variable that displays the location of the genome sequence files on the file system, as well as other details of available genome sequences.
For more details on this variable and how to use the Participant Explorer please see our documentation, which we will also update on Tuesday.

If you have any problems using this tool after this update please raise a service desk ticket. You can also use the service desk portal to leave feedback on the Research Environment.
We apologize for any inconvenience this outage may cause.

Best wishes,
The GeCIP Team

Research Environment and HPC outage: 18:00 12/11/2020 – 18:00 15/11/2020

  

Dear Users,

The Research Environment will be unavailable to perform some essential maintenance 18:00 Friday 13th November – 18:00 Sunday 15th November.

The HPC (Helix) will be unavailable one day earlier from 18:00 Thursday 12th November to 18:00 Sunday 15th November.

We will be carrying out the HPC work on Sunday 15th, but we are pausing access to the HPC three days in advance to allow jobs to complete prior to the work.

Please avoid submitting any long-running jobs this week. If your job is still ongoing by Sunday 15th, it will be killed. In the event that you have a job that must be killed, you will be contacted directly letting you know it needs to be restarted.

If you try to submit a job to the HPC during the outage, the job will be held and will then be executed once the maintenance is finished. 

We apologise for this disruption, if this outage will significantly impact your work or if you have any further queries, please contact our Service Desk: [email protected].

Reminder: You can view the archive of these Research Environment alerts here and upcoming and live service issues here.


Best wishes,


Genomics England

HPC outage Halloween weekend

 

Dear Users,

We regret to inform you that urgent maintenance is required for the Research Environment's storage system and it will be entirely unavailable 10.00-17.00, 31 October 2020. During this time you will be unable to read or write files inside the Research Environment and all ongoing jobs submitted to the HPC will be killed. Please do not submit any jobs to the HPC before the outage. If you try to submit a job during the outage, it will be held and begin once the maintenance is over.
If you have an ongoing job that is killed due to this maintenance, one of our engineers will contact you directly and you will need to restart the job once the maintenance is complete.
We sincerely apologise for the disruption to your work. We would not do this on such short notice were it not absolutely necessary and we will endeavour to give you more notice for any future disruptions of service.


Best wishes,
Genomics England

Participant Explorer Update

 

Dear Users,

We will be updating the Participant Explorer including the latest v10 data, as well as some bug fixes. The application will be unavailable during the update, the estimated outage will be 9am-1pm 19/10/2020 (today).

We apologise if this interrupts your work at all.

Best wishes, 
Genomics England

Research Environment outage 13/10/2020

 

Dear Users,

The Research Environment will be down for a few hours tomorrow morning to install an important update.

The down time is expected to be from 7am - 9am on 13/10/2020.

If you have any problems accessing the Research Environment after these times, the update may be taking longer than expected. If you are still having problems logging in until later in the day please raise a service desk ticket.

Best wishes,
The GeCIP team


New scratch directory for temporary files

  

Dear Users,

We have seen exponential data growth in the Research Environment, and this has become increasingly expensive and unsustainable. Therefore, we have now made available a scratch directory which you can start using today for any temporary files.

Via the HPC (Helix), you can write to the file path /re_scratch/re_gecip/[domain_name] or /re_scratch/discovery_forum/[company_name]. The storage limit on /re_scratch will be much larger than that on /re_gecip, so you will be able to store large temporary outputs here.

Genomics England does not guarantee the retention of data on the scratch drive after one month, so please keep this in mind whenever storing files there.

We hope this will be helpful tool for you in running your analyses while optimising data storage.

Best wishes,
Genomics England

Data Discovery Portal update - 06/10/2020

 

Dear Users,

The Data Discovery Portal application is being updated to include data from the v10 data release, as well as new COVID-19 attributes.

In order to implement this update we will have to take this app down from 9am tomorrow (06/10/2020).

We expect this outage to take a minimum of six hours but we hope to have the app up and running again with this new data and features by tomorrow afternoon.

If you feel that this may substantially affect your work please raise a service desk ticket to provide feedback or direct this to the GeCIP team directly at [email protected].

Best wishes, 
The GeCIP team.

Confluence currently down

 

Dear Users,

Confluence inside the Research Environment is temporarily unavailable. Apologies for the inconvenience; we are expecting it to be available again before the end of the week. If you need to access any of the documentation during this time, you will still be able to access the version outside the Research Environment at https://cnfl.extge.co.uk/display/GERE.

We also remind you that the Research Registry can now be found on the new Research Portal: visit https://research.genomicsengland.co.uk outside the Research Environment.

Best wishes,
Genomics England


Genome permission access resolved

 

Dear Users,

We had noticed that, shortly after introducing Data Release v10, users experienced issues with access to genomes. Restricted access largely involved the newly released realigned genomes and long-read sequencing data, although some individual genomes were also affected.

We have resolved the issue and users should now be able to access these accordingly. We apologise for the inconvenience and delay this has caused in your work.

Please reach out to us via the Genomics England Service Desk in case you are still experiencing issues with access to the new genomes.

Kind regards,
Genomics England

New Main Programme Data Release v10

 

Dear Research Environment Users,

Today we completed a new data release from the main programme of the 100,000 Genomes Project, consisting of rare disease and cancer participants.

To help you use this data and understand what is available, we have published a data release note, which you can access here<Release v10 (03/09/2020)>, as well as in the Research Environment User Guide in the Documentation within the Research Environment. Please also note:
• This release contains all of the genomes sequenced as part of the 100,000 Genomes Project. Bringing the total number of genomes available to 111,232 total, 32,224 from cancer and 74,008 from rare disease. This also increases the total number of clinical data points to 3.9 billion.
• Out of all the rare disease genomes in this release, those that are already tiered (61,138) have undergone full in-house quality checks and are derived from a pool of genomes for which family checks are available (as the first step in our tiering process). Of the cancer genomes, 31,590 have also undergone full in-house quality checks, which means that, in total, 92,728 genomes in this data release are fully quality checked.
• There is a significant 25% increase in GMC exit questionnaires since last release, with exit questionnaires are now available for 25,071 families. This is where you can find information about which genetic variants, if any, the GMC considered to be responsible for the participant’s disorder.

What’s new in this data release?
This data release will include the last batch of genomes recruited through the 100,000 Genomes Project as we move towards our new programme, the Genomic Medicine Service. This takes the total number of genomes available to 111,232, with 37,224 in Cancer and 74,008 in Rare Disease. Other significant updates include bringing in COVID-19 diagnosis data for participants of the 100,000 Genomes Project – with more data on severity from intensive care units to follow soon. COVID-19 diagnosis data will continue to be added for 100,000 Genomes Project participants subsequent to this release at a greater frequency than the main programme data release. The Data Discovery Portal within the Research Environment has also been updated to include COVID-19 as a disease for filtering cohorts.

It is our great pleasure to release a new aggregated multi-sample VCF dataset – termed the aggV2 – containing 78,195 germline genomes from our 100K participants (GRCh38). This is one of the largest whole genome aggregate datasets currently available in the world. As with our previous aggregate, a full summary table with sample stats is available in LabKey, and extensive documentation is provided here, including a handy codebook to assist with your queries!
In this release we will also be bringing in updates to our secondary data including Mental Health Services Data Set (MHSDS) and Systemic Anti-Cancer Therapy (SACT). There will also be significant improvements to the cancer clinical dataset now that real time data is being used to improve the uncurated SACT feed. We will of course continue to have subsequent data releases including more secondary data, and once the Genomic Medicine Service is fully established, this data will flow into the Research Environment
Other new items that we are introducing into the Research Environment with this release, are the samples sequenced with Oxford Nanopore Technologies, providing long-read sequencing data for 49 of our participants. Beyond the long-read sequencing data we are also providing access to genomic data realigned with the new Dragen pipeline for almost 2,000 genomes. Be sure to check out our Release Notes to see how and where you can find these on LabKey.
Finally, with Release Version 10 we are also introducing workflows for our users, with the aim to making our data more easily accessible for users with ranging coding experience from beginner to advanced. More details can be found here.
Research Environment Application Data
Please note that not all applications in the Research Environment are aligned to the latest data release, please refer to the following to documentation to view what data version each application is using: Application Data Versions.
Returning potentially clinically actionable variants
If you find a variant you think is clinically actionable during your research, don’t forget to let us know by completing the “Researcher-identified potential diagnoses form” within the Research Environment!

Best wishes,
Genomics England

The Research Registry has moved

 

Dear Users,

The Research Registry has now moved and is housed within the Research Portal (https://research.genomicsengland.co.uk/) outside of the Research Environment. This new Research Registry has been significantly improved to expedite the review process and also includes a sophisticated advanced search that enables you to find projects using a query builder. Improving the search functionality means that it will be easier to find research projects related to your area of interest and form collaborations, as well as preventing potential duplication of effort. You should be able to log in to the Research Portal using the same credentials you use to access the Research Environment. This is only the beta version of the Research Portal, so if you encounter any issues, have any ideas to improve the Portal, or you require any further assistance, please do not hesitate to contact the Genomics England Service Desk. Please include “Research Portal” in the subject line of your Service Desk ticket.

Best wishes,
Genomics England

 

Microsoft Office 2013 applications now available!

 

Dear Research Environment users,

We are excited to announce that Microsoft Office 2013 applications will now be accessible within the Research Environment!
This means that users will be able to access Microsoft Word, PowerPoint and Excel from icons on the desktop or from the start menu. 
You should now be able to open files created using LibreOffice from within Microsoft Office applications.
If you have any problems using these apps or cannot see them please raise a ticket in our service desk portal at https://jiraservicedesk.extge.co.uk/ or by emailing [email protected].

Best wishes,
The GeCIP team

Research Registry temporarily unavailable

 

Dear Users,

The Research Registry form will be temporarily unavailable for the next few days, preventing any new project submissions. This is to perform some essential work in preparation for the launch of the new Research Registry that will be housed outside of the Research Environment. You will be able to resume submitting projects Tuesday 4th August 2020.
If this will significantly impact your work, please raise a Service Desk ticket.

Best wishes,
Genomics England.

COVID-19 test data

 

Dear User,

We are happy to announce that we have released the first two batches of COVID-19 testing data for 100,000 Genomes Project participants. These data can be found in LabKey, in the “Frequent Release” project (at the same level as Main Programme). The data give information on the time of tests, specimen types, laboratories, requesting organisations, positive/negative test results and any dates of death. There are data on 4543 test results, linked to Participant IDs. A data dictionary for these data can be found here. Further COVID-19 data on Project participants will be released into the Research Environment as part of the regular Main Programme data releases, the next of which is anticipated for the end of August. Updates at shorter intervals will be provided into the Frequent Release LabKey project.  In order to perform analysis on these data, please remember to register a project in the Research Registry for approval first, if you have not already done so.

Best wishes,
Genomics England

OpenCGA/IVA v2 go-live note to RE Users

 

Dear Research Environment users,

We are delighted to announce the release of the latest version of OpenCGA/IVA variant store! This release increases both usability and performance compared with the previous version. The IVA web application can be launched using the desktop icon or navigating to http://re-iva-prod.gel.zone. The command line interface can be loaded in terminal using "module load opencga" command. Existing Python and R clients need to be configured to use the new URL: re-opencga-prod.gel.zone. The platform initially provides data from the Rare Disease Programme (v8 release). Data includes 45,403 genomes (samples) from 21,344 cases (families). The dataset is in two studies; GRCh37 (12,167 samples, 5,237 families) and GRCh38 (33,236 samples, 16,107 families). GRCh37 contains 322,533,290 unique, normalised variants and GRCh38 contains 435,756,262.

Please contact Genomics England Service Desk https://jiraservicedesk.extge.co.uk/ for any issues or support, and for feedback/ suggestions for further development - select the IVA option.

Coming over the next few weeks;
Revamped documentation
More genomes; addition of Cancer Programme data and update to Main Programme release v9.
Greater functionality; we will be developing a user engagement programme.

Best wishes,
The GeCIP team

Using the new HPC (Helix)

 

Dear Users,

We have recently migrated all researchers to the new HPC Helix. You should have received an email update in the past few weeks. We are working on a complete rewrite of the HPC documentation in the User Guide which we hope to release soon. However, in the meantime we want to refer you to the following page: navigating to the external Research Environment User Guide (outside of the RE) (https://cnfl.extge.co.uk/display/GERE/) > Live Service Issues > HPC (Helix) Migration 2020.

The process of loading modules remains similar, but the names of specific modules may have been adjusted. Please type "module avail" on the Helix HPC to see the current list of modules, so you can adjust your scripts accordingly.

Should you want to request new software to be installed, you can still do so through the regular software request tickets selecting the HPC Pegasus option. We will consider these requests for HPC Helix.

If you have not received an e-mail concerning your migration (please check your junk mail), please reach out to us via the Genomics England Service Desk.

Best wishes,
Genomics England

IVA and OpenCGA Upgrade

 

Dear Users,

Please note that IVA[*] version 1.0.3 and OpenCGA[†] v1.4.2 will soon be upgraded to IVA v2.0.0 and OpenCGA v2.0.0. We will also change our cloud provider to Micorosft Azure. The switchover between versions is scheduled for 13th July 2020 – we will provide more specific timings closer to the date. No action is required from you, other than ensuring you are no longer connected to either application on that day. However, there will initially be changes to the samples available within OpenCGA v2, so we ask that you complete any work involving IVA by Friday 10th July. Following the successful deployment of the new platform based on OpenCGA v2.0.0 and IVA v2.0.0, the desktop link to launch IVA will be updated, as will the Python and R libraries, and the CLI client.

Initially, OpenCGA v2 will contain only the rare disease genomes currently available in the Research Environment (i.e. the GRCh38 cancer somatic and germline genomes will initially not be available). This is a temporary situation that we will resolve before the end of July. As we move further into the Summer, we will not only offer all the data currently hosted by OpenCGA (both cancer and rare disease), we will also add the remaining rare disease and cancer genomes from the 100,000 genomes project that have yet to be made available in the Research Environment. More details on this will be made available here: /gel_data_resources/main_programme/opencga/available_genomes

Finally, and importantly, you should be aware that given the significant changes (major upgrades to the software, and the switch to our new cloud hosting), there is likely going to be a period of downtime in the week commencing 13th July. We will work strenuously to minimise the downtime, and we will make every effort to restore service at the earliest opportunity. Nevertheless, it is advisable that any work that relies on the existing instance of OpenCGA and IVA be completed by the end of Friday July 10th.

Kind regards, 
Genomics England

Urgent: Please reduce your data storage

Dear All,

We have noticed a recent increase in the amount of storage being used, and are very close to reaching maximum capacity.

Please: 
Do NOT copy BAM files from the by-date folder for any reason. If you have already done this please let us know.
Please discuss with us before you run any job that will generate a large amount of data, e.g. (but not limited to) new BAM files.
Please reduce your folders by deleting files you no longer need. We will soon be setting quotas at 50-100Tb for each domain. If your individual folder is approaching 50Tb (or bigger!) it will need to be reduced urgently. If this will be a problem, please contact [email protected].

Many thanks for your cooperation. We will be providing info soon on good practice in use of our HPC. We will also be providing a scratch directory for temporary storage of files.

Best wishes,
Anna Need and the GeCIP team.


Folders in re_gecip - privacy settings

 

Dear GeCIP members,

It has come to our attention that since the storage migration at the beginning of October, some folders in the shared re_gecip directory have had their privacy settings restored to public. 
If you have created a folder within re_gecip and restricted access to you only, please now check it is still restricted and reset if necessary. Sorry for any inconvenience this has caused.

Warm wishes, 
The GeCIP Team


New data release (v8) now available

 

On the 28th November we completed a new data release from the main programme of the 100,000 Genomes Project, consisting of rare disease and cancer participants. There are 107,513 genomes available from 89,335 participants.
Click here to read the data release note to find out about the new data available in this release, including cancer staging data, which is now available for 62% of interpreted cancer genomes, compared to 30% in the last data release.

As of 5pm on the 28th November, some files from the cancer_analysis table that are deposited in the gel_data_resources folder are still in the process of being copied over. We expect that this will be completed by Friday 29th of November at approximately 9am. The LabKey table for Version 8 is up-to-date and correct. Apologies for any inconvenience caused.

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