The first public beta version of pLink 2 is released!
Zhenlin Chen
Dear pLink users,
Happy new year 2018!
It has been six years since pLink 1 was released in 2012. Over the past years, we have more than 900 registered users and 280 citations. More importantly, pLink 1 was used as a tool in 70 published studies. We thank you for your choosing pLink 1 and we are very glad that pLink 1 has contributed positively to research.
Although pLink 1 works, you may have found that it is not as user-friendly as it should be, and not fast enough by today’s standards. Over the past several years we have been working hard to develop pLink 2 to give pLink 1 a thorough upgrade. Here we are happy to announce that pLink 2 has passed numerous tests with a shiny record and this brand-new software tool now stands ready to serve the research community. Compared with pLink 1, pLink 2 has many advantages:
1. Fast: built on a new index structure and a new search strategy, it is ~40 times faster than pLink 1.
2. Flexible: support various types of cross-links including those generated by cleavable or non-cleavable chemical cross-linkers (e.g. DSS, DSSO), disulfide bonds, and SUMO modifications.
3. Friendly: a wizard-like graphical user interface to help users create tasks and set up workflows.
4. Powerful: support large protein databases (e.g. human) with > 8 GB RAM.
5. Precise: identification quality is further enhanced by a new re-ranking algorithm and systematic validations.
6. Quantitative: with a seamless connection of identification and quantitation algorithms, come and enjoy a smooth ride in quantitative cross-linking data analysis using stable isotope labeling of either cross-linkers (Leiker) or proteins (15N).
As such, we are excited to launch pLink 2. This new and powerful software tool will be released on January 1, 2018, at http://pfind.ict.ac.cn/software/pLink2/index.html. Like pLink 1, it is free for academic users.
As pLink 2 can do everything pLink 1 does, and do more and better, our official support of pLink 1 ends with the year of 2017. If you have on-going projects that demand the continued use of pLink 1, please contact us.
pLink has a discussion group on Google Groups, but it is inconvenient for us to access the messages posted there. We thus have moved the pLink discussion group to GitHub: https://github.com/pFindStudio/pLink2/issues. You can contact us by email (pL...@ict.ac.cn) or leave a message in the pLink 2 repository. Any comments, questions, and bug reports are welcome. Please see github.pdf for GitHub usage.
Again, thank you for using pLink! We eagerly invite you to try pLink 2, which we think will bring you a smooth, joyful experience in data analysis. We hope to see you again in the expanding community of pLink 2.
Happy New Year and Happy Research,
The pLink Team of pFind Lab
Institute of Computing Technology
Chinese Academy of Sciences
