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Happy Holidays! Looking back at 2013 and forward to 2014 …
December 23, 2013 by Vijay Pande ·
As the year ends, it’s a natural time to look at some key highlights of we’ve done in 2013 and look ahead to what’s on deck for 2014. One of the challenges of science results can easily take a year for us to run on FAH, analyze, and publish. So, the work of 2012 comes out in 2013 and the projects running in 2013 get to reach the public in 2014. So, it makes sense to talk about both work that’s been going on this year and how all of this will shape up in 2014. We’ve been doing a lot behind the scenes in 2013 and I’m excited about all of this getting out to the public in 2014. Here are some key developments.
FAH development in 2013. We’ve had several new developments in how FAH works, from both the donor perspective as well as how FAH works behind the scenes. With the addition of new programmer Yutong “Proteneer” Zhao, Core 17 was a big advance for FAH. It brought the most advanced features from the OpenMM GPU code, especially major speed increases for AMD/ATI cards. Moreover, it also brought a natural path to true Linux GPU support and lots of useful scientific updates. The v7 client continues to advance, with a new web interface; these simplifications have been important especially for certain partners who have wanted to see an easier to use FAH client before they can help us push for greater deployment. Adaptive sampling approaches have been a part of how FAH works, but we’ve also been moving to automate this process, leading to more powerful ways we can use the power of the FAH clients.
New FAH results. Several of our long running projects have come to fruition in 2013 and gotten various honors. One major result which also gives a good idea of where we’re going in the future was our work on GPCRs, key proteins at the heart of much of disease and drug design. Our work on GPCRs, running a FAH-like infrastructure on Google’s internal processors, sets the stage for similar calculations to be run on FAH (as I’ll describe below). In a nutshell, what we’ve been able to show is that the tools used to understand protein folding (developed in FAH) can shed light on how GPCRs behave, especially revealing intermediate structures which are interesting and potentially important new targets for drug design.
New projects. Kinases are key drug targets for cancer. 2013 brought new projects which will lead to new papers in 2014. Many donors have asked us to push into more areas in cancer and our pilot projects have worked out well, leading to full fledged FAH projects in cancer. Our first paper in this area has been submitted, with several more in the pipeline. I’ll post more when the paper is out, but briefly, we’ve been able simulate kinase dynamics, identifying new intermediate states that could be useful drug targets. Our goal is to help develop kinase drugs with greater specificity, leading to a dramatic improvement in cancer therapies, especially without the devastating issues of current chemotherapies, which comes from the fact that current drugs are not very specific to a give kinase and affect the whole body—not just the tumor cells—in a very negative manner. We also now have some very high power collaborators on board, including those at the Memorial Sloan Kettering Cancer Center in New York. We also have new results in Alzheimer’s Disease and Infectious Disease which we are in the process of submitting for publication. These results are in the area of drug repurposing, leading to the ability of the FAH team to go straight to therapies for these diseases using combinations of existing drugs; we’ve very excited about this direction as it allows us to go quickly to phase 2 clinical trials, getting new drugs in the hands of patients decades before other methods would.
Looking to the future of FAH: on deck for 2014. We’ve been working behind the scenes with various partners to get Folding@home disseminated into more people’s hands, increasing what we can all do together. We expect to release a whole new type of client and backend server in 2014, which will help make it easier and easier for many donors to contribute to FAH. Also, we’ve gotten a lot of useful responses to the donor survey and we’re working to implement the most important suggestions. Specifically, we’re hiring a new position solely for donor relations. We hope that this will solve the challenge of the science team having to decide between donor relations and getting their science done, by having someone whose sole role is donor relations. Finally, we have several partnerships with companies who have been working to promote Folding@home that we will hopefully be able to announce in 2014.
For us, it’s a very exciting time. 2013 was very much a year of laying seeds for 2014. The key elements are an improved client and more powerful set of cores (especially GPU core17) combined with new backend methods, applied to key new scientific projects running in 2013 in the areas cancer, Alzheimer’s Disease, and infectious disease. All of this, pushed forward by a lot of raw power from partnering could easily make 2014 a landmark year for FAH. We’d like to thank all of the donors who make this possible and look forward to hopefully working together to make 2014 the best year FAH has ever seen.
大意：
剩蛋快乐之2013年终总结。
又到年底了，该写年终总结了，我们也不例外。一般情况下我们计算、分析、发表论文大概要1年时间，所以13年的成就大部分来自于12年的工作，而今年的工作，要到14年才有体现。那么现在就让我们回顾过去，展望未来吧。
2013总结之开发篇。由于赵宇桐的加盟，开发了core 17版GPU内核，给显卡计算效率带来质的飞跃，同时也加入很多新功能，也对linux GPU提供了原生支持。V7客户端加入了网页界面，简化了操作。同时为FAH加入了智能采样算法，让我们能更好的利用FAH的计算力（译注：我也不太清楚这是个什么东东）。
2013总结之新结果。利用谷歌的内部服务器集群，我们对GPCRs进行了详细研究，为将来的药物设计研究打下坚实基础。
2013总结之新项目。很多志愿者要我们加强癌症方面的研究力度，而激酶是抗癌药物的关键，所以2013年的工作重心放在了激酶上。第一篇论文已经提交了，其他后续文章正在积极准备中。一旦有新消息我会及时告知大家。通过对激酶的研究，我们发现了很多新的可用于药物研发的中间态。这可以使将来研发的药物，更具有靶向性，效果更佳。（众所周知，目前普遍使用的化疗，木有靶向性，不但攻击癌细胞，也攻击正常细胞，副作用极大）。而且Memorial Sloan Kettering癌症研究中心的加盟，也使我们如虎添翼。老年痴呆症和传染病方面的研究也有重大突破，新论文正在发表中。研究的主要方向是药物重利用，即在现有药物中寻找可以混合起来治疗疾病的鸡尾酒新药。这样‘新药’就可以直接进行2期临床阶段，这种方法至少比其他方法能提前十年进入临床使用。
展望2014：希望能加大宣传让更多的人加入FAH。发布新的更加人性化的客户端和服务器端。专门雇佣了志愿者关系维护人员，搞好与志愿者们的沟通（译注：看到这句，我蛋疼的不行了！）。2014将有更多的合作者加盟。
就剩一句了：2013主要升级了客户端和内核（尤其是core 17）。项目方面主要研究了癌症、老年痴呆症、传染病。在更多服务器集群加盟的情况下，FAH的算力将取得突破。希望和大家共创2014年的辉煌。谢谢大家！ |
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发表于 2013-12-24 16:00:10
发表于 2013-12-24 16:27:39