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| About FAQ Below is a list of frequently asked questions (FAQ) with answers from the ProteomeCommons.org admin. |
The following are commonly asked questions about the purpose, developers, and supporters of ProteomeCommons.org.
ProteomeCommons.org is a public repository for digital content relating to proteomics, and a foundation for building a community around such content. We provide public access to free, open-source proteomics-related projects both new and old. ProteomeCommons.org was founded on the idea of helping the proteomics community grow, and this continues to be our primary focus.
Dr. Philip Andrews, Jayson Falkner, and Pete Ulintz (Dept. of Biological Chemistry, University of Michigan), are the original creators of ProteomeCommons.org, and the project was conceived collectively by the three in order to support their open-source proteome informatics efforts.
When it comes down to business, Phil is the Primary Investigator who supports Jayson and Pete. Jayson does all of the coding and graphics work, and Pete helps with news and links.
The content and ideas expressed by ProteomeCommons.org are a collective effort of the proteomics community. Funding for ProteomeCommons.org comes in part from the National Center for Proteomics and Pathways.
All entries in the ProteomeCommons.org repository come with a signed hash, meaning you can always verify that you've got an exact copy of any archive being kept in ProteomeCommons.org. Hashes are done using SHA and encryption is done with DSA using our private key. You may use any conventional hash/encryption software to check these values, but we recommend using the latest version of the ArchiveChecker project, which may be downloaded from the archives.
Please note. While you can verify that a file you download is an exact copy of a valid archive, there is no way to validate any given archive is well-suited for any particular purpose. We try our best to hand-validate entries as reasonable projects when they enter the repository, but ProteomeCommons.org does nothing more than host a copy of other people's work. Consult the authors of the particular archive file if you have questions or comments about it.
You should try using the ProteomeCommons.org e-mail list. This e-mail list is the appropriate place to ask questions about this website or about any of the projects on it. Most of the main developers are on this list along with many different users. If you are having a problem, odds are you'll find quick help here.
You may also try to get in touch directly with the project's developers via the e-mail address associated with the project. Sometimes this is a great way to get feedback from the people who wrote the code, but you are encouraged to try the e-mail list first. We normally advise developers who are bogged down with work to point user inquires to this FAQ as a quick, polite way to ask you to try using the ProteomeCommons.org e-mail list.
The ProteomeCommons.org e-mail list is the official mechanism for news, announcement,s and community discussion about this web site. It is open to the public and if you are interested in ProteomeCommons.org, you should subscribe to the e-mail list. the e-mail list is powered by Google Groups and you many search through old e-mails using Google.
Note: You may elect to have e-mail sent individually or in digest form. Select digest form if you are worried that you'll get alot of e-mail from the ProteomeCommons.org e-mail list. Digest will send you one summary e-mail per day.
If you would like to join the site's e-mail list, go to the Google Groups webpage. Note, we will keep your e-mail address information private, and you may unsubscribe yourself at any time. Any attempts to solicit products or use the e-mail list for non-ProteomeCommons.org related issues will result in removal of your e-mail from the list.
There are a few reasons that we have chosen to decorate the site with cake. One of the key concepts people don't seem to get is that free, open-source software is really both free to use and you can down the complete source-code. If you imagine free, open-source software as cake it is like the saying goes, "You can have your cake and eat it too." Another motivation for the cake is that it has absolutely nothing to do with biology, computers, or proteins. We figure that you've seen enough of those websites decorated with gaudy twirling peices of DNA.
You'll notice that the cake theme will change from time to time, including which images appear mixed in with the cakes. We figure that there are a lot of fun things we can do with cake, and we'll be trying them all. Expect to see plenty of pictorial puns along with silly images of those who actively help with the proteomics community.
ProteomeCommons.org provides web-based downloads, i.e. using nothing but your web browser, as either one compressed ZIP file that contains all of a single project or as individual, uncompressed files from a project. In general, material that you download from ProteomeCommons.org is both free to download and free to use; however, each project is licensed under specific open-source terms to ensure that it is used fairly and that credit is appropriately given to the project's authors. See the specific licensing information that is bundled with each project before you use the code.
To download a project, select the project from the archive entries and click on the link that ends with ".zip" and is to the right of the "Download:" text. To download any of the individual files from a project, simply click on the file's name. All files in a project as listed in the detail page for the project.
If you are downloading big files, it is suggested that you use bittorrent. You downloads may be much faster.
SHA and MD5 are support files for a particular project that you can use to ensure that a project's contents haven't been tampered with. MD5 well known hashing algorithm that can be used to verify a file hasn't changed. We provide MD5 sums for all project files. SHA is a digital signature algoritm that ensures both that a file hasn't been changed and that it comes from a particular source (e.g. ProteomeCommons.org in our case). We provide a SHA signature for all project files. If you don't already know how to use MD5 and SHA or you don't have the software readily available and you'd like to use MD5 or SHA, you may freely download and use the ProteomeCommons.org ArchiveChecker project.
The following are questions that developers commonly ask about ProteomeCommons.org.
ProteomeCommons.org is a good, free, public method of sharing your proteomics software and data sets. If you'd like to put your source-code or data set on-line and do a good job of it, ProteomeCommons.org is fine choice for the following reasons.
No, but we do for some. ProteomeCommons.org has several subversion repositories and e-mail lists that developers may use. See the development page for more information.
For projects we actively develop here at ProteomeCommons.org you can always get the latest source-code via the subversion repository. See the development page for more information. Note, that development versions of code are not actively supported, nor are they encouraged for use. Use formal releases (i.e. archives) if you want stable code.
See the development page for information about submitting patches and bug reports.
We are always looking for good developers. The best thing to do is to get yourself known by getting involved with some of the projects we actively develop. Then get in touch with the site's administrators.
Go ahead, we won't stop you. ProteomeCommons.org is nothing more than a community support site. We do not claim any rights to your code or data. You are free to host your own projects in any way that you please, and we'll even try to help. Let us know when you've set up your own site, and we'll mirror your code so that users can take advantage of the ProteomeCommons.org servers' bandwidth.
Alternatively, you may consider hosting your complete website at ProteomeCommons.org. Any HTML page that you embed in a project will be publically available to the World Wide Web, i.e. we'll host the website for you. Additionally, we use bittorrent to provide a distributed system for project mirroring and download acceleration. If you have a server, you can mirror your own project and your users will benefit. Just because your project is hosted at ProteomeCommons.org doesn't mean everything has to be on our servers.
Comments or Questions? Please contact the site's administrators.