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TN-Grid
2023-12-29: Happy New Year!

Just a very brief update: People here are working on submitting papers, analyzing the FANTOM and Vitis vinifera data and so on. A nice Web application to look and play with the results is almost ready. Unfortunately there is yet no ETA on the new experiments to be done here.
Happy New Year to everybody listening!

2023-07-10: Summer break

I just put the last Vitis vinifera genes into our queue. With the current pace it will take about a week, maybe less, to distribute them all. The new datasets are not ready yet... Also, I will be on vacation the next two weeks, and it wouldn't be advisable to start a new work without having the possibility to easily oversee the system.
Therefore, in a few days, the work generator will not be able to produce new tasks, only resends will be floating around.
I hope to be able to restart the system with a new project at the beginning of August.

Thank you all!

2023-05-15: The Vespucci-2023 Vitis vinifera OneGenE experiment

The Vespucci-2023 Vitis vinifera OneGenE experiment is officially started, for more scientific info about it please look at this thread https://gene.disi.unitn.it/test/forum_thread.php?id=370.
Thank you all for your support!

2023-04-28: Maintenance (filesystem and o.s.)

Right now that our queue is empty it is the perfect time to switch our filesystem to the new one and to upgrade the operating system of the server. This will probably happen the 2nd of May, for a couple of days. During this period the server may be down for awhile. After that, if everything will go smoothly, we plan to start distributing work again.

2023-04-07: The end of the FANTOM-1 experiment

At our current pace the remaining workunits related to the very long and computational intensive OneGenE FANTOM-1 experiment (started in March 2018) will be distributed in more or less two days. This will be the end of this job.

For the future of the gene@home project please look at this thread
https://gene.disi.unitn.it/test/forum_thread.php?id=366

2023-03-02: Storage problem (again)

As all of you already know we are constantly struggling with our problematic storage. The University have bought a new one and they planned the moving procedure. The HPC cluster should be moved this Monday (March, 6th), the other resources will follow.
I will reasonably shut down the server when needed, I will tell you when as soon as I know the date. Meanwhile the work generator will be active just a few hours a day, so very few workunits will be available.
Thank you all for your understanding and patience.

2021-11-23: Paper published on Biomolecules

Although the current focus of our job is on the Homo sapiens genome, in the recent past we also ran some gene expansion experiments on the Vitis vinifera organism. We are still evaluating those results, in collaboration with the Edmund Mach Foundation and the Universitat de Val

2021-10-14: Storage problem

The University's storage system (that we heavily use) is having big performance issues thus everything is painfully slow. I stopped the work generator, which actually was not working because of this. No new tasks will be generated until the assimilator will be able to move the finished results to the proper place. There is nothing else to do but wait until the problem will be solved, no ETA, unfortunately.

2021-03-02: World Gene Expansion Challenge 2021

The volunteers belonging to the BOINC.Italy group have organized the usual (end of winter) challenge on this project: Start: 8th March 2021 12:00 UTC, End : 15th March 2021 12:00 UTC.

Please follow this thread for further info https://gene.disi.unitn.it/test/forum_thread.php?id=307

2020-10-16: Paper published on IEEE Transactions on Emerging Topics in Computing

The following article, "A Computing System for Discovering Causal Relationships among Human Genes to Improve Drug Repositioning," is available under the "Early Access" area on IEEE Xplore. This article has been accepted for publication in a future issue of this journal, but has not been edited and content may change prior to final publication. This paper appears in: IEEE Transactions on Emerging Topics in Computing, Digital Object Identifier: 10.1109/TETC.2020.3031024. You may find it here: https://ieeexplore.ieee.org/document/9224179
Thank you all for your invaluable support!

2020-09-16: AMD COVID-19 HPC Fund Adds New Research Institutions

Our gene@home project (hosted by the University of Trento, Italy) has been chosen by AMD as a recipient for their COVID-19 HPC fund, see the official announcement https://www.amd.com/en/corporate/hpc-fund

We are really grateful to receive this donation, it will give us access to high performance computing nodes, boosting our research. More info and comments here: https://gene.disi.unitn.it/test/forum_thread.php?id=291

2020-09-08: Server unreachable (2020-09-09, from 05:30 to 08:00 CEST)

Wednesday 09/09, from 05:30 to 08:00 CEST, the IT services of UniTrento will not be available because of a planned IT maintenance. The TN-Grid server (hosted by UniTrento) will probably be not reachable during this period.

2020-02-21: World Gene Expansion Challenge 2020

The volunteers belonging to the BOINC.Italy group have organized a challenge on this project, from March 16 at 12:00 UTC up to March 23 at 12:00 UTC.

Have a look at the challenge banner here: https://www.boincitaly.org/media/kunena/attachments/6725/TN-GridCh.jpg and the boincstats announcement/chat page: https://www.boincstats.com/stats/challenge/team/chat/1072

2020-02-13: No news is good news (sometimes)

Just wanted to say that everything is going on smoothly. The server is stable, the scientists are happy with the results and are doing their analysis. Thanks all!

2018-12-21: Server stop for maintenance (2018-12-27, 9:30 CEST)

The next 27th December the server will be down for some planned maintenance tasks, starting at around 9:30 CEST (GMT+1). The most important will be upgrading the o.s. to the latest stable release. Hopefully, the server will be back online the afternoon of the same day.

2018-11-23: Planned maintenance

We will shut down the server the next Monday (November 26) at 12:00 CEST (GMT+1) for some planned maintenance work. The stop should last less than on hour.

2018-10-24: Publication about Vitis vinifera

A new scientific paper on Vitis vinifera has been published. Details here: https://gene.disi.unitn.it/test//forum_thread.php?id=225

2018-05-11: New organism

The experiments on Vitis vinifera are almost finished, thank you all. We will soon switch to a new organism. We made some tests some time ago but we found that the outputs of the Windows and Linux applications didn't match each other. The new forthcoming Windows applications should behave correctly.
The next Monday we will distribute them and (slowly) start creating new work.

2018-04-20: Server down this weekend

Our storage system (managed by the University) has some serious problem. They are working to fix it but they cannot estimate for how long it will be down. We decided to stop the server at least until the next Monday.
Thank you for your understanding.

2017-12-05: New application (v 1.10)

A new application version will be distributed soon, starting with the Linux platforms. The new application contains some major speed enhancements and bug fixes. Look at the following thread for further info http://gene.disi.unitn.it/test/forum_thread.php?id=135.

2017-10-18: Another experiment on E. coli

We are ready to start another experiment on Escherichia coli, using the same expression dataset of the previous one but changing one of the algorithm's parameters.
Execution times should slightly faster than the last one on Vitis vinifera.

2017-06-29: Vitis vinifera: new dataset

We are starting to distribute another experiment (single gene expansion) with a new Vitis vinifera dataset. This dataset contains the same number of genes but a much larger expression data; running times are therefore expected to be much longer (around twice).

2017-03-14: Restarting

We rebuilt some parts of the whole system and are almost ready to go full speed. Please look at the following thread https://gene.disi.unitn.it/test/forum_thread.php?id=165#952

2017-03-02: No new work

I decided to stop the work generator until we solve our storage problems and have the new application (small output files). Most of our systems are now busy just moving things from here to there, this also implies a lot of (boring) micromanagement.
Hope you all understand.

2017-02-06: New application (v 0.11)

In the next few hours the new v1.1 optimized applications made by Daniel will be promoted as the official ones (version 0.11). This version is faster than the previous one. If you are using the anonymous platform and want to safely 'come back' remember to: wait until the workunits queue is empty, stop boinc, delete app_info.xml, start boinc.

2017-01-13: New application (v 0.10)

We are deploying the new version of the application (v 0.10), for all the platforms, including sse2, avx and fma. The new application is way faster than the previous one, thanks to the user Daniel who made it. See this thread (http://gene.disi.unitn.it/test/forum_thread.php?id=135) for further info.

2017-01-05: Workunits length

I've recently doubled the size of the workunits. Credits should scale up accordingly.

2016-12-21: SSL Certificate

In the next days I will install a SSL certificate, thus allowing secure communications via the https protocol. You may notice it when your boinc client will start complaining about it, saying something like "This project is using an old URL. When convenient...". You may simply ignore this message or detach from the project and re-attach using the new https url (it will be the usual one, just with https:// at the beginning).
Please do this when your queue is empty.

2016-12-02: First international challenge on TN-Grid

The BOINC.Italy Team has opened the first international challenge on this project.
Title: "Despite my age I don't live in the past, but in the future" 4th Rita Levi-Montalcini memorial and 30 years from Nobel Prize.
Start 10 Dec 16.00 UTC - End 16 Dec 16.00 UTC
Check http://boincstats.com/en/stats/challenge/team/chat/831 for more info.

2016-11-29: Badges

Credit badges are now available, please check the following thread http://gene.disi.unitn.it/test/forum_thread.php?id=130#608

2016-11-10: Upgrading the server

Today, in about 1 hour from now we will shutdown the server for an upgrade (ram, cpu and storage). It shouldn't take a long time, maybe one hour or less. [edit] Everything went well.

2016-10-11: tn-grid: Public invitation code

The (new) invitation code is now public, written on the home page.

2016-10-11: Public invitation code

The (new) invitation code is now public, written on the home page.

2015-12-24: gene@home: Vitis Vinifera experiments

We just started a new 'experiment' on a Vitis Vinifera (grapevine) dataset. Your client will automatically download a ~100Mb files which contains the necessary dataset (shared among all the Vv workunits). We will distribute just a few batches, at the beginning, just to see if everything works as expected.

For further (scientific) information please look at the following thread: http://gene.disi.unitn.it/test/forum_thread.php?id=117

2015-06-10: gene@home: Scientific Results (June 2015)

We are very happy to share the scientific results achieved so far, thanks to the help of all you volunteers. Please look at this thread.

2015-03-07: gene@home: status

We are almost done with our current batch (E. Coli local gene network expansion for 10 networks). We will first analyze the results (this will take some time), then we will be able to choose the best, smaller set of algorithm parameters and use it for the other 100 networks we plan to expand, thus optimizing the computation. In the meantime we will start another experiment on Arabidopsis Thaliana but, before starting it, we need to wait until all the work on E. coli has been generated. This will be done manually, hopefully the next Monday.
For this reason there could be a shortage of workunits in this weekend.

2015-02-25: gene@home: Server down next Friday, February 27th

Dear users,
due to maintenance work in the datacenter, we need to temporarily switch off the server. The machine will not be accessible next Friday, February 27th, starting from 9am (CEST). We don't now how long will it take to bring the server up, hopefully just a few hours. Thank you all for your understanding.

2014-12-22: gene@home: Holidays are approaching

The winter holiday break will shortly begin, it will be from the 24th December to the 6th of January. During this time the server will (hopefully) be up and there will be plenty of jobs. However, in case of any problems it will be very difficult for us to fix them (a lot of people will be on vacation and also my office will be closed). Season's greetings (and a big thank) to everyone!

2014-12-09: gene@home: Server down the 14th December

There will be some server downtime the next 14th December (Sunday). The data-center hosting the server will be moved (physically) to another building. We don't know exact timing nor for how long the server will be down.

2014-11-20: gene@home: Re-issue of old 'experiments'

Due to a partial storage hardware failure we need to redo some old experiments. We already used the results we got for the paper we are writing, therefore we need to keep the raw data for future reference. This old work will produce workunits which name starts with N_At_fos (with N less than 100).

2014-11-12: gene@home: Escherichia coli experiments (Update)

We distributed a small batch of E. Coli workunits (their names contain the 'Ec' string). Unfortunately our algorithm for the estimation of the running time is not working for them. So, until we'll fix this, the 'remaining (estimated) time' you see on the boinc manager will be underestimated by a factor of 2 to 10. However, despite of this, the workunits will run fine.

2014-11-07: gene@home: Escherichia coli experiments

We are starting a new series of experiments on a new organism, Escherichia coli, with the goal of mapping the complete gene network of this prokaryote. We just started to distribute a small set of workunits for testing the system. We already find some problems: the boinc client 'estimated time remaining' seems completely wrong (too short, almost zero) although the progress bar is normally stepping up, we will see...

[UPDATE] We aborted/canceled them all... They ended all with the 'Maximum elapsed time exceeded' error... we have to fix this before going further.

2014-10-08: gene@home: October update

This project is partially linked to the Laboratory of Biological Data Mining class of the Master's course in Computer Science at our University. Now the class has started. The students need a little bit more knowledge of the whole system before starting new 'experiments', thus creating new work. We all think that another couple of weeks will be needed.

2014-08-11: gene@home: August news

We are not yet ready to start new 'experiments', i.e. delivering new workunits. We were focusing on writing a paper about the algorithm we use (it's almost ready). Now it's exam time for students and vacation time for a lot of people so I declare the project as 'suspended' until the mid of September.

2014-06-25: gene@home: Planning new 'experiments'

We are waiting for all the recently distributed workunits to come back (just one missing by now) before taking some time to analyze the results and planning new work distribution. We are still in the validation/testing phase of the algorithm we developed, we have obviously to check it thoroughly before going into the production phase. In the meantime we are writing a scientific paper describing it and this also takes some time. However, expect some more news at the beginning of the next week. Thanks all again for your help.

2014-06-05: gene@home: Leave one out phase

Dear all,
we started a new phase for leave-one-out processing. Our goal is to evaluate the recall of our algorithm w.r.t. different parameters. We removed from the starting local gene network one gene at time in order to see if we are able to find it.

Have a nice crunching, and thanks to all! :)

2014-05-27: gene@home: Break! Post-processing phase

Hi all gene@home supporters!
We just empty our experiments queue, do not worry new works will be available soon! ;-)
For the moment we are collecting and processing all the results (just few are not yet come back). We are also checking the feedback provided for the application, in order to see if there are things that should be fixed or improved.
We hope in a few days to put here http://gene.disi.unitn.it/test/forum_forum.php?id=2 some results from this last experiments.

Thank you all for crunching! :)

2014-05-22: gene@home: Parameters tuning reloaded

In order to validate our algorithm, we started several experiments, friendly called "empty" (because they didn't have a local gene network that will be expanded).
These experiments should tell us the impact of the "divide-et-impera" approach performing inference, with respect to the expansion done within every subgraphs.

2014-05-16: gene@home: Parameters tuning reloaded

We posted a gif of the most significant plots we obtained from the first phase of parameters tuning here: http://gene.disi.unitn.it/test/forum_thread.php?id=85

I really like scientific news!!
Good job, boys!

2014-05-14: gene@home: Parameters tuning reloaded

To the initial work programmed for this second phase of parameters tuning, we added a quite big deal of experiments.
In fact, at the end of the last week we received a new local gene network related to flavonoids. This was a good news because we can expand this new local gene network using the same input used for the first local gene network (FOS), since both of them are related to the flowering of the Arabidopsis thaliana.

We posted a gif of the most significant plots we obtained from the first phase of parameters tuning here: http://gene.disi.unitn.it/test/forum_thread.php?id=85

Enjoy!

2014-05-09: gene@home: Parameters tuning reloaded

State: All (306) · In progress (110) · Validation pending (43) · Validation inconclusive (0) · Valid (153) · Invalid (0) · Error (0)

2014-05-09: gene@home: Parameters tuning reloaded

As usual use the forum if there are any problems.

Over 20 wus ok, only 1 "validation inconclusive"
828

2014-05-08: gene@home: Parameters tuning reloaded

We have scheduled more than 10000 (ten thousands! :) ) workunits for a second phase of parameters tuning.
We are trying different parameters' values, hence the time estimation could be not always correct.
As usual use the forum if there are any problems.

Have a nice work!
Thank you all!

2014-04-17: gene@home: Presentation @ ICT-Days 2014

The gene@home project has been briefly presented at the Transversal Technologies Section of the ICT-Days http://2014.ictdays.it/ held in Trento at the beginning of April 2014, here is the presentation http://gene.disi.unitn.it/test/documents/geneAThome.ICT.Days.2014.pdf

2014-04-03: gene@home: Parameters tuning

We started a new test phase where we are tuning the application parameters. We are currently expanding a flowering process of the Arabidopsis thaliana.
As usual use the forum for reporting problems.
Thank you.

2014-03-25: gene@home: Solved not unique download filename

Hi there,
we should have solved the issues arise yesterday related to the not unique filename generated by the work generator.

We also update the application in order to get a bette stderr from the executions.

Let us know if there are still problems,
Thank you all for the support!

2014-03-24: gene@home: Testing the new system

We just put on the queue about 1000 workunits for testing the new system. The work generator was completely rewritten and also the application has been modified a lot. We hope that we solved (almost) all the problems we found in the past. Let's see. A more detailed changelog will shortly follow. As usual, feedback will be very appreciated. Thanks all for helping us in this projects.