Status of this BioCompanion edition:
This UNIX version is called 3.2.7, created
in November, 1996. GCG9 features are active. Seqlab is emphasized.
This BioCompanion copy is the GCG CD copyrighted version
.
This section is intended for the interested researcher who is new to the field, and wants
to get familiar with the prerequisites. The BioCompanion assumes that you own a computer and
work in a networked environment (including access to the
Internet ). You are expected to use a local network to
a more centralised facility provided in-house or in a reasonable (network) distance.
If you do not currently have access to the Internet, a few items might not apply as described.
However, hints will be provided at the appropriate sections to alert you if networks are used
outside of your organisation. Most of the work is achieved locally, and executed on local equipment.
Special hints on security are inserted wherever appropriate to make you aware of the problems
in internationally accessible environments.
No matter whether you work at a university
or industrial place, the days of a terminal which connects to a mainframe
are gone. Your PC or Mac might even be powerful enough to run some of the required software
on the desk without any need for remote facilities. However, due to the economies of scale and
the general pace of development, BioInformatics today is almost certainly implemented on a network
of computers. This might be a network in your office or building (
Local Area network , also called LAN), a whole environment at your campus (also called
an Intranet ), and it might be the international Internet .
There are some implications with international networking and the BioCompanion will refer to
these issues at the appropriate section items.
This section of the BioCompanion explains the prerequisites that have to be
met to do BioInformatics. This will never be a precise introduction because of the complexity
of the matter, but, basically, two scenarios are either coexisting or used separately:
Main issue: Your data are local to your local desktop PC, and you will manipulate
it typically using the PC or Mac tools
Main Issue: Your data are typically remotely stored and handled. The typical
GCG setup is such an example.
To use the typical Bioinformatics environment, you should have
NOTE: In the past, connections to central facilities using "terminals" were widely used.
This method of access is no longer recommended as it usually excludes the use of graphics. Many
programs still utilise text modus and are supported as well, but the access via personal computers
or even workstations should be favoured. Personal computers are, depending on age and equipment,
hybrids of terminals and workstations.
The access to facilities using the X-Windows protocol is only essential if you intend to run
the SeqLab product of the
GCG software package (Introduced with GCG version 9.x). If you use GCG Version 8.x, the so-called
WPI will be employed. Both programs are explained
later . SeqLab is a very different product than WPI which you might have been using before.
If you did not, why don't you have a look and see whether the SeqLab is a better way of working.
Briefly, SeqLab allows you to work in a graphical environment and allows to select sequences
in a so-called list . Depending on its mode , you can use single
sequences and sequence groups in the programs (selected from pull-down menus), or you switch
to edit mode and can enter, modify and manipulate sequences, groups of sequences
or alignments. The main benefit of the SeqLab editing mode is its capability
to use colors for various properties, such as strand orientation, amino acid properties, and
inter-sequence similarities. Features can also be displayed if annotated in
the sequences, and color-coded accordingly. To achieve this functionality, SeqLab
uses X-Windows to display the mouse-driven User Interface. The BioCompanion
describes the sections explicitly where the unique concepts of SeqLab can be efficiently used.
Bioinformatics is very data- and compute intensive, and therefore
cannot be performed easily (in terms of economy and performance) on the individual researcher's
PC. You will work on a central computer or departmental workstation that is maintained as a local
resource for Bioinformatics.
Option 1: Access to a remote computer via WWW
With the emerging World-Wide Web technology it is typically
essential to have access to a functional
as many help text facilities, program interfaces and network information is provided using this
technology.
Unfortunately, today's WWW browsers might not be as standardized as required in order to use
a remote site efficiently, and you will need the most recent version of a certain browser's brand
eventually. Do not mix up the two approaches of an interactive login at a remote host,
which you need to store files, manipulate sequences, etc. and the
client/server connection which occurs if you use
WWW and possibly other tools. The latter will allow you to "browse" remote sources of information
or even databases, typically without authorisation (sometimes, usernames and passwords are required
as described below).
The GCG software package does not currently run via WWW in its standard configuration.
Access via Internet to many (non-GCG) computing services is currently possible
with WWW tools.
SECURITY ADVICE
Make sure that you are familiar with the internet access policies at your site. In commercial
environments, access to internet tools is PROHIBITED because of a potential violation of security
interests.
Do not rely on a remote Internet site if your research depends on it without having made sure
that the use of this resource will be possible throughout your project. WWW resources might vanish
without avdance notice if you do not have an account/username on the remote computer. This is
because the service provider does not know whom to inform about changes in service provision.
Do not mix up IntrAnet (the internal network) and Internet (the international network) - it is
possible that your site offers secure, in-house services via WWW which are not affected by security
considerations.
A WWW interface is very convenient to use but the data are typically stored locally
- this implies that remote data analysis requires either to upload data
via a certain mechanism or cut and paste facilities. There is a special
section on WWW access in this chapter.
To use such a system in very sophisticated fashion you might also need an
Option 2: Access to a remote computer via Telnet or X-Windows
Alternatively to WWW, you might use electronic networks to access resources at remote sites via
a virual terminal (telnet) or a windowed environment (X-Windows) .
Usually, you will share this remote computer with (many) others. Yours and the data of your colleagues
are also stored on the same machine. At large sites, a computer can have hundreds of users. Therefore,
these computers run a
multi-user operating system . To access such a system, you must have the following prerequisites:
Ask your nearest computer knowledgeable person for details about where to get this information.
As mentioned, the use of SeqLab requires (on the desktop side) to display the windows sent by the GCG software. More
details on access are provided below.
Many computing services in academia
are offered for free or negotiable cost to the end user. Nevertheless, costs will need to be
covered by someone. In commercial environments, and, to an increasing extent in some institutions
in academia, subscription fees will need to be paid in order to allow to access
resources. It is essential that you understand that your research is important, and that the
price of computational resources is low compared to the potential loss of valuable information.
Computing services are typically paid for by centralized organizations (such as a computer center)
or department. The individual researcher is affected only indirectly.
Hardware
(like PCs, terminals, and local printers) and software
(like word processors, X-servers and
terminal emulators ) residing on your desk usually have to be provided by you or your lab
or department. Be careful if you use local area networks for
software installation - if in doubt, ask your local network administrator for details on licensing.
SECURITY
ADVICE: Do not install software over the network if you are not sure
whether you are authorised to do so. Software piracy is punishable by law. If you download software
from the Internet, make sure that no implications on your local environment might result. Specifically,
check for viruses and other malicious code.
If the network
connection appears to be unsatisfactory (e.g., too slow, too "difficult", etc.), 'better'
links are unlikely to be installed readily. Try the existing ones first before complaining. If
you cannot get an account on a system where molecular biology and
other software is installed, you are in a less favourable position, because you will have to
organise everything yourself. See below for details of the
desktop setup with respect to potential pitfalls and prerequisites.
At some places, you may use either the campus-maintained systems or the workstations run at the
individual departments. The functionality of both types of systems is often equivalent. You might
need to find out where the next specialist is on hand to get you information where to access
the molecular biology packages on a suitable host. In European academia, you
can try to approach your nearest EMBnet node for information.
[next page] , or [overview] , or [table of contents] Needed Equipment
Desktop
On-Site or Remote Central Computing Facilities
Prices
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