[项目]The Lattice Project (1#更新研究报告PDF链接)

Julian_Yuen

呃，搜索了一下，似乎论坛里面关于这个的相关信息很少（也可能我没有搜索出来...）
http://www.equn.com/forum/viewth ... 6&highlight=Lattice
http://www.equn.com/forum/viewth ... 37&page=1#pid188045

项目网址  http://boinc.umiacs.umd.edu/

项目状态  http://boinc.umiacs.umd.edu/server_status.php

关于本项目  http://boinc.umiacs.umd.edu/about.php
开始于2003年末，持续至今，由马里兰大学开发，本意是为了自身的科研需要，但开发者认识到了BOINC平台的巨大优势，并认为BOINC社区有可能是Lattice的最有潜力的计算资源。Lattice正在以BOINC平台为基础，转移原有项目并为之开发适合于BOINC平台的新程序。

该项目下目前包含的计算程序    http://boinc.umiacs.umd.edu/apps.php

研究内容
Here are some of the projects and analyses being run on Lattice.

    * The Cummings Laboratory and others are using GARLI to infer evolutionary relationships based on DNA sequence data.

    * The Edwards laboratory is using the HMMPfam service to compute Pfam assignments for all bacterial, plasmid, and virus protein sequences from Swiss-Prot, TrEMBL, GenBank, RefSeq, and TIGR's CMR, plus an inclusive set of all plausible Glimmer predictions from RefSeq bacterial genomes. These protein sequences, and their Pfam assignments, are used in the Rapid Microorganism Identification Database (www.RMIDb.org). The HMMPfam service is also being used as a model for "data-heavy" bioinformatics applications on the Lattice Grid infrastructure, a collaboration between the Cummings and Edwards laboratories.

• N.J. Edwards and F. Pineda. Poster at ASMS (2006). Rapid Microorganism Identification Database (www.RMIDb.org), 2006.

    * Dr. Catherine Dibble's Computational Laboratories Group uses agent-based simulation models to study the geographic spread of Avian Influenza across the United States, to quantify the relative pandemic risk of US cities and determine optimal intervention strategies. The Grid service being used is Complab.

• Catherine Dibble, Stephen Wendel, and Kristofor Carle (University ofMaryland). Simulating Pandemic Influenza Risks of U.S. Cities. In Proceedings of the 2007 Winter Simulation Conference, 2007.

    * The Cummings Laboratory is using gsi to assess the performance of the statistic in a variety of situations.

    * Maile Neel and Joanna Grand are using Marxan to quantify the effects of poor and incomplete data on the ability to capture biological diversity in nature reserves.

• Grand, J., M. P. Cummings, A. G. Rebelo, T. H. Ricketts, and M. C.Neel. 2007. Biased data reduce efficiency and effectiveness ofconservation reserve networks.Ecology Letters 10:364-374.

    * The Laboratory of David Fushman is running protein:protein docking algorithms on Lattice. When driven by experimentally derived constraints, these will help in modeling the structures of large multi-subunit proteins, and the interactions of such proteins with various ligands. CNS is the featured Grid service in this project.

• Varadan, R., Assfalg, M., Raasi, S., Pickart, C. & Fushman, D.Structural Determinants for Selective Recognition of a Lys48-LinkedPolyubiquitin Chain by a UBA Domain. Mol Cell 18, 687-98 (2005).

    * Floyd Reed and Holly Mortensen from the Laboratory of Sarah Tishkoff have run a number of MDIV and IM simulations through The Lattice Project. These are studies in molecular population genetics that seek to use DNA sequence polymorphism to estimate the times of divergence and migration rates among ethnically diverse human populations in Africa.

• Tishkoff, S. A., Gonder, M. K., Henn, B. M., Mortensen, H., Knight, A.,Gignoux, C., Fernandopulle, N., Lema, G., Nyambo, T. B., Ramakrishnan,U., Floyd A. Reed, F. A. & Mountain, J. L.History of Click-Speaking Populations of Africa Inferred from mtDNA and Y Chromosome Genetic Variation. Molecular Biology and Evolution 24(10), 2180-2195 (2007).

==================================
研究内容

以下是Lattice平台上运行的一些项目及分析。
    * 卡明斯实验室(Cummings Laboratory)正在与他人一同通过GARLI来推论基于DNA序列数据的进化关系。

    * 爱德华兹实验室(Edwards laboratory)正在使用HMMPfam服务(HMMPfam service)来计算来自Swiss-Prot、TrEMBL、GenBank、RefSeq和TIGR's CMR的所有细菌、质粒以及病毒蛋白质序列的Pfam课题(Pfam assignments)，并包括来自RefSeq细菌基因组的所有不确定的预言。这些蛋白质序列，以及它们的Pfam课题，将被用于快速微生物鉴别数据库(www.RMIDb.org)。HMMPfam服务也会作为Lattice基础网格的一个用于“大数据量的”生物信息学程序的模型。该网格由卡明斯实验室和爱德华兹实验室协作完成。

    * 凯瑟琳.迪博尔博士(Dr. Catherine Dibble)的计算实验室组通过基于媒介的仿真模型来研究禽流感在美国地域上的地理学蔓延过程，以期量化相关的全国流行的风险，并决定最佳干涉策略。目前被使用的网格服务是Complab。

    * 卡明斯实验室(Cummings Laboratory)通过gsi来获得不同情形下的统计数据。

    * Maile Neel 和 Joanna Grand通过使用Marxan来量化在自然保护区中所记录的生物差异的贫乏的、不完全的资料的效果。

    * 大卫弗斯曼实验室(Laboratory of David Fushman)正在Lattice平台上运行蛋白质对接算法(protein:protein docking algorithms)。受来自于实验条件的局限所迫，该算法将有助于模拟巨大的多分子蛋白质的结构，以及蛋白质与不同配合基的相互作用。CNS是该项目中具有代表性的网格服务。

    * 来自莎拉提斯科夫实验室(Laboratory of Sarah Tishkoff)的 Floyd Reed 以及 Holly Mortensen 正通过Lattice项目来进行若干MDIV和IM的仿真模拟，他们运用分子的群体遗传学(molecular population genetics)，以期通过DNA序列的多态现象来对非洲变化多样的人口的趋异分散和迁徙移动的次数进行估计。

[ 本帖最后由 Julian_Yuen 于 2007-12-15 17:12 编辑 ]

Julian_Yuen

June 13, 2007
All of the work for this batch is in the system. The output from the newly released Windows version differs slightly from the other platforms, unfortunately, so I'm going to turn homogeneous redundancy for HMMPfam back on at some point. For those whose results were marked invalid recently, we're sorry.

June 9, 2007
To all who participated in our first test, thanks. I also appreciate the feedback on the message boards. We have a second wave of work going in now that is approximately 16 times bigger than the first one, so it should keep everyone busy for a while! For information on this research, look here.

June 7, 2007
All, you should now point your clients to http://boinc.umiacs.umd.edu/. We will have a small to moderate amount of work in the system shortly. This will be our first test with public clients since the project was re-launched, so we'll see what happens. However, this is real data, not test data! Good luck, everybody.

June 4, 2007
I didn't see a reason not to allow new accounts to be created at this point, so go right ahead, and post something if you encounter problems. However, do not try to attach to the project - it won't work just yet! I'll send another notice when the project URL is activated.

May 31, 2007
We're currently trying out the new HMMPfam application. Hopefully within a couple of weeks we'll be ready to turn it loose on everyone. As the day draws near, we'll open up account creation again so all can get ready. Thanks for your patience and continued interest!

May 11, 2007
Within a few weeks, we'll probably open up the project again in some limited capacity in order to test a new application, which is a part of the HMMER suite. This should give everyone something to look forward to!

April 17, 2007
We've noticed you found the site. We are currently working on polishing up the site's features, so expect changes and things to break. We've disabled account creation and client connections for the time being. We may or may not reply to message board posts. And it's uncertain when real work will be flowing through the system again, but we'll keep you posted...
Sincerely, The Lattice Project Team

[ 本帖最后由 Julian_Yuen 于 2007-6-19 16:07 编辑 ]

Youth

才发现这个项目可以注册用户

而且很奇怪有个Yin Gang的帐号3 Aug 2005就有了...是我吗?

Youth

晕倒，试了半天果然是我以前用另外一个邮箱注册的，居然还建了team，完全没有印象...

Julian_Yuen

呃，呵呵，我看到没有Team China，又怕以后发生Seti那样的情况，就先保护性注册了，呵呵~

Youth

呵呵，我已经加team china了，反正原来的那个team也一分都没有算过：）

Julian_Yuen

这个项目也不知道是干什么的，我也只算了一点点一点点，呃，好像似乎也是个平台（没仔细看）....
依据：Here are some of the projects and analyses being run on Lattice.

diablo2

只参加医疗项目～

其他项目都不考虑～

Julian_Yuen

docking该怎么翻译？

BiscuiT

对接

diablo2

.......

Julian_Yuen

原帖由 BiscuiT 于 2007-6-28 14:11 发表
对接

原来如此

work in a docking environment

.....就是说在一个对接的环境中工作

呃，一直不知道这个怎么翻译好

Julian_Yuen

June 23, 2007
Versions of HMMPfam approximately 3x faster have been released for all platforms except Windows, which is soon to come.

June 21, 2007
I have increased the number of results available in the feeder's shared memory segment from 384 to 3840, so you should see the "there was work, but it was committed to other platforms" message more less frequently!

June 15, 2007
I have increased the number of results available in the feeder's shared memory segment from 100 to 384, and I've set it to purge stale WUs every ten minutes instead of every thirty. You should hopefully see the "there was work, but it was committed to other platforms" message less frequently now.

June 15, 2007
I just released a few workunits which contain an error that causes the HMMPfam application to terminate immediately, quite probably putting some of your clients into an endless loop. If you're affected, just reset your project, and my apologies.

June 13, 2007
We have word that a batch of HMMPfam six times larger than the most recent batch is on its way. Look for it in the next couple of days!

Julian_Yuen

June 28, 2007 Turning On HR Once Again
Regretfully, we are turning on homogeneous redundancy for HMMPfam once again because there are simply too many inconsistencies, numerical and otherwise, that are causing results to be marked as invalid. Plans to release a native BOINC version are on hold pending developer time to work on a Windows version.

June 26, 2007 Turning off HR
A new Windows version has been released which should correct some formatting differences in the output. Therefore, homogeneous redundancy has been turned off, but we will be monitoring any validation errors that occur. It's also worth mentioning that we are working on a wrapper-less, native BOINC version of HMMPfam that will do checkpointing. Stay tuned!

June 23, 2007 Faster HMMPfam Versions Released
The 3x faster version of HMMPfam has been released for Windows. We are continuing to modify the source so that we may be able to turn off HR for this application eventually. We are approximately 40% of the way through this batch of work, but we are cutting off the flow of work into the system for a short time. Thanks for your continued interest in the project!

Julian_Yuen

July 5, 2007 GARLI Trials
Soon we will be releasing some GARLI workunits into the wild. We have an experiment outlined that will require several thousand workunits crunched, in due time. Initially, HR will be turned off for GARLI.

GARLI 测试
我们将释出一些GARLI的WU。我们大概需要处理数千个测试WU。HR也会关闭，为了GARLI。


July 9, 2007 GARLI Trials
The deadline for these workunits has been made 5 days, and this should be enforced on any new workunits that are created.

GARLI 测试
这些测试WU的上报期限被设置为5天。而且所有新的WU也都将使用这一设置。

[ 本帖最后由 Julian_Yuen 于 2007-7-11 22:57 编辑 ]