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[项目新闻] [BOINC] [生命科学类] TN-Grid

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发表于 2020-7-9 00:28:08 | 显示全部楼层 |阅读模式
本帖最后由 xhl1212 于 2020-7-9 00:27 编辑

跑了这个项目几个月,没看到有人在这里讨论,我发个帖子介绍一下吧

TN-Grid is a platform that uses Internet-connected computers to do research in various scientific projects. You can participate by downloading and running a free program on your computer.
TN-Grid is based at the Research Area of Trento of the National Research Council of Italy (CNR) and currently hosted by the University of Trento (UNITN). The first project we host is
  • gene@home, in collaboration with Fondazione Edmund Mach (FEM) and the Department of Information Engineering and Computer Science (DISI) of UNITN.
We would also like to thank the members of the BOINC.Italy community who were very helpful for starting this project.

项目主页:http://gene.disi.unitn.it/test/

这个项目由意大利国家研究委员会发起,理论上是个类似WCG的平台,但是从2013年到现在只有一个子项目gene@home,子项目主要研究生物基因,介绍在这里http://gene.disi.unitn.it/test/genehome/en/hf/index.php
Gene@home is a scientific project belonging to the infrastructure TrentoGrid. It is aimed to expand networks of genes, and to perform this task it exploits the computational power of volunteers through the BOINC platform, which allows distributed computing.
The experiment is done on the plant Arabidopsis Thaliana.


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 楼主| 发表于 2020-7-9 00:32:49 | 显示全部楼层
本帖最后由 xhl1212 于 2020-7-9 00:37 编辑

项目关于新冠病毒基因研究的进展
http://gene.disi.unitn.it/test/forum_thread.php?id=265

消息 1698 - 发表于:14 Mar 2020, 19:07:17 UTC - 回复消息 1697.
We are actually expanding a lot of human genes, prioritizing them according to the scientists' interests. Among them this one (ACE2) https://www.ncbi.nlm.nih.gov/gene/59272 which is closely related to the SARS-CoV-2 virus. Don't expect we will be able to 'find a cure' but we are trying to add something to better know our enemy.

In the mean time, please, take care.


消息 1712 - 发表于:19 Mar 2020, 23:08:59 UTC
We just added some other genes related to ACE2, according to this https://string-db.org/cgi/network.pl?taskId=fBQjTFzroyIX

They are AGT AGTR1 AGTR2 REN MME DPP4 PRCP MEP1B MEP1A XPNPEP2, among them we already expanded MME and DPP4. You may see the others' names coded inside the workunits string.


消息 1726 - 发表于:28 Mar 2020, 23:01:43 UTC
最近的修改日期:28 Mar 2020, 23:02:11 UTC
Added a few genes, related to DPP4, according to StringDB:
INS GIP SLC5A2 SLC5A5 ADA GCG GLP1R


消息 1731 - 发表于:2 Apr 2020, 10:57:27 UTC - 回复消息 1727.
I just put into the queue all the genes related to SARS-CoV-2 according to this paper https://www.biorxiv.org/content/10.1101/2020.03.22.002386v3

The data we used are available here https://public.ndexbio.org/#/networkset/4b4a9769-6ad1-11ea-bfdc-0ac135e8bacf?accesskey=abb250cd4e341423f3e913d71c171068c75c722e54649a83868feff7f239a548


Description: Interactomes for SARS-CoV-2 (coronavirus) the virus causing COVID-19. Interactomes have been performed in multiple cell lines, including HEK-293T, and a lung cell line, A549.

Workunit's id will start at 165735_Hs to 166977_Hs, that's the expansion of 1242 gene isoforms, each one will be 294 workunits, so there is plenty of work to do...


消息 1742 - 发表于:3 Apr 2020, 16:00:13 UTC - 回复消息 1740.
最近的修改日期:3 Apr 2020, 19:55:46 UTC
We already published the OneGenE (expansion of all the genes) results for a Vitis vinifera dataset (Vespucci).

The OneGeneE project for Homo sapiens FANTOM-5 gene expression dataset is our 'background' job, and it is a very long one. We normally put genes in the queue in alphabetic order (actually it is by 'number of isoforms', but it would be the same). At the very beginning we started by prioritizing genes related to neurovegetative diseases, then to some types of cancer, right now any gene possibly related to COVID-19 (you guess why...).

Any result we get is immediately available to the scientific community (biologists etc.), for example the ACE2 expansions we completed a few days ago will soon be analyzed by a immunologist, etc.

We are also studying the possibility of doing some work on specific gene datasets recently made up from cells of SARS-CoV-2 infected individuals. In this case we will put 'on hold' the OneGenE Hs project.


消息 1808 - 发表于:28 Apr 2020, 9:38:47 UTC - 回复消息 1807.

Already received work from other batches ahead of 166977.
Are these still SARS-CoV-2 related or from the Homo Sapiens (OneGenE - FANTOM-1) data set?

mixed, for now, for instance ENPEP and TMPRSS2 should be related to SARS-CoV-2. Keep in mind that all genes/isoforms are taken from the FANTOM dataset. We are prioritizing those (human) genes related to the Covid-19 disease, infection and/or pathology.


消息 1850 - 发表于:25 May 2020, 16:54:30 UTC - 回复消息 1833.
The first batch of genes related to COVID-19 has been completed. We sent the results, for further analysis, to the Univ. of Modena & Reggio Emilia School of Medicine, Italy. Starting from today we added another batch of genes, per request of the aforementioned institution. Most of them are antibodies, so the focus right now is the immune system.

Here is the list of the genes: PTPRC CD28 CCR7 PDCD1 SNCA SPATA2 CD27 B3GAT1 IL7 IL2RA ISG20 FAS PTPN13 CD38 CD74 CD24 CR2


 楼主| 发表于 2020-7-9 00:41:25 | 显示全部楼层
注意:这个项目不能直接从BOINC客户端创建账户,需要先在这个页面创建账户,然后加到BOINC客户端里:https://gene.disi.unitn.it/test//create_account_form.php
第一行Invitation Code填science@tn
 楼主| 发表于 2020-9-17 07:20:46 | 显示全部楼层
gene@home新冠项目已得到AMD赞助,官网已更新

TN-Grid Platform: 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
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