Documentation:FAQ

I'm a new member and I'm lost?

Start by reading Documentation:FAQ carefully. Browse CompBio wiki as well as http://compbio.washington.edu. Specifically the Documentation:Joining and Documentation:Information may be the most relevant.

I can't find my answer in the FAQ?

Try one of the following:

• Search the CompBio wiki (or compbiki) at http://wiki.compbio.org.

• Do a Google search of the Web restricted to our domains and/or the group archives. We need to put up a google search analytics on the main compbio web page (I think it is there now), but there is one for ram.org. However you can go to the main Google page and search for pages within a single domain. You can search under compbio.washington.edu or ram.org or the samudrala-compbio Google group. If you know your query is related to a specific topic for which we have a domain, you can search under that, for example CANDO related items are likely to be under protinfo.org/cando, Bioverse under bioverse.org; Protinfo under protinfo.org and so on. However this is by no means a hard and fast rule since CANDO, Bioverse, Protinfo, and even CompBio and ram.org are all interconnected in a tangled hierarchy. This is most apparent in our web pages that cross reference extensively; see our group philosophies for further detail. So it may be better to just broadly search google for queries of interest but in the end there's no substitution

• See our glossary and index.

The Web pages seem to be extensive; why a FAQ?

In short, too many people asking the same questions and repeating the same mistakes again and again. The point of the FAQ is to consolidate different sources of information under one window. It is not just pointers to pointers like a glossary or a FAQ but also delves into the semantics a bit deeper. For example, you may find a piece of information that is not documented or poorly documented.

I found a piece of information that is not documented or poorly documented?

You're reading the answer. You can add it to this FAQ; create a new page; clarify it in other relevant pages; write an email to the corresponding people and/or the group list (always a good idea). There are other ways you can help further.

How may I help?

These are questions for which there is no one unified answer yet in this FAQ; please feel free to start an answer to them. There are also numerous missing links, typographical errors, and other corrections that could be done in the wiki and elsewhere. Correcting information in the wiki is trivial and works like editing any Wikipedia article. To correct our other pages, please contact one of our system administrators. If you wish to provide a proof of concept, then it is better to edit your HTML page using a *simple* HTML editor (usually by hand) and then having the new format laid out for people to see. This can be done using the wiki. Be sure to read our documentation and follow our style guides and other relevant documentation if you are asking and answering a new question.

What are some good practices for email communication?

Any means of communication and discussion is okay for a dialetic and email is one such means. Since a copy of each email goes to every user's mailbox, avoid the use of redundant information and instead just provide pointers to them. Remember that people use smartphones, speech to text to speech, and other ways of communicating and assimilating information. Assuming people can see colours, mathematical equations, or anything sophisticated like a MS Word or other MS Office document is unwarranted. Not to mention that some of us simply avoid MS products due to their relative inefficiency from the outset. It can take several seconds to open an MS Office object even on a powerful laptop and forget about even being able to view htem on a smart phone or listening to them at the beach by automagic text to speech conversion. Thus be cogent of the audience you're communicating. This applies with all walks of life, not just email.

All of us probably get more email than we could read patiently even if we had our entire lifetimes. As a result, some of us, including Ram, prioritise the reading of email such that the clearest minimalist (not the same as minimal) pieces of communication get read first. This means email that is in plain ASCII with no attachments, no proprietary formats, no HTML formatting, and so on will be most likely to be read and answered. If you wonder specifically why Ram takes a while to respond, this is the most likely reason since he scrupulously tries to avoid being inefficient with Spock-like determination.

What do you mean by minimalism and being minimalist?

Minimalism means being minimalist. In general, the theme of minimalism will arise constantly in CompBio. When in doubt, it's always good to be minimalist. Minimalism, to coopt Einstein, means that you should be as minimal as needed and no more or no less.

What are some good practices for computing?

Minimalism again is key. With computing, it's really important to use only the tools you need minimally that work for you. A single bit more is wasteful. Efficiency can be overreated also and it is important to maintain an equilibrium. For example, you could spend so much time being perfect that you accomplish nothing. Conversely, you could be so carefree and easy going that you accomplish nothing. Like with everything else referenced in this FAQ, a *dynamic equiilbrium or homeostasis* is necessary between these states for real efficiency and productivity when that is the desired goal.

For example, if Ram had all the time in the world he claims he'd read all the emails in the way they were sent leisurely, but since he gets way more emails than he can possibly read in their entirety the way they were sent even if he had his entire life time, he is likely to get to emails that are minimalist in nature. To clarify and emphasise, a *dynamic equilibrium* does NOT mean a 50/50 split. It just means that it's the equilibrium that maximises the benefit functions while minimising the cost functions simultaneously.

I'm confused by the use of the group mailing lists?

(No answer yet.)