Illinois Bio Grid Glossary

Our own wikipedia of bioinformatics and grid terms

• Also see Other BioInformatics glossaries

BioInformatics Glossary

ab initio

A way of calculating molecular dynamics for the purpose of a simulation, those calculations being based on the basic chemical properties (such as covalent bonds, hydrogen bonds, van der waals forces, etc.)

amino acid

The basic build block of a protein. For decades, there were thought to be only 20 amino acids that comprise all proteins. Recently, however (2002?), rumors of a 21st amino acid are circulating. There are several ways to categorize amino acids: hydrophobic vs. hydrophilic, relatively large vs. relatively small, etc. The sequence of amino acids in a protein determine how the protein will fold in three dimensions.

ANDI/NetCDF

The ASMS (American Society for Mass Spectrometry) approved file format standard for data transfer that all MS manufacturers are expected to be able to export to. Few manufacturers actually support this format, as it was never able to handle multidimensional MSn data.

Base Peak Chromatogram (BPC)

A (mass spec) chromatogram in which the y-axis for each point on the chromatogram represents the intensity of the most abundant ion in the mass spectrum underlying that point. (See “Mass Spectrogram”)

Chromatogram

A separation of substrates, usually proteins, by some method that keeps like substrates together but separates each from other different substrates. For example, a Liquid Column Chromatogram is a long cylindrical glass tube mounted vertically and filled with extremely small glass beads. Proteins dissolved in water is added in at the top and then water is drawn off at the bottom into a different test tube every 10 minutes or so. The smaller proteins can get through the glass beads quicker than the larger proteins, so the smaller proteins will be in a test tube drawn at an earlier time from the bottom of the column. (See “Mass Spectrogram”)

DeNovo or de novo or denovo

Extracted Ion Chromatogram (EIC)

A (mass spec) chromatogram in which the intensity (y-axis) for each data point on the x-axis (time) reflects the intensity for just one ion in the underlying mass spectrum at that data point. The user specifies the mass to be used for extracting the chromatogram. (See “Mass Spectrogram”)

GC/MS

Gas Chromatograph Mass Spec - The instrument separates compounds using a gas chromatograph, and then each compound is run through the Mass Spec to get its molecular weight.

in silico

A term biologists use to describe a process occurring in a computer, as opposed to in vivo or in vitro

LC MS

Liquid Chromatograph Mass Spec - The instrument separates compounds using a liquid chromatograph, and then each compound is run through the Mass Spec to get its molecular weight.

LC/MS/MS

Liquid Chromatograph Mass Spec Mass Spec (recursive)- The instrument separates compounds using a liquid chromatograph, and then each compound is run through the Mass Spec to get its molecular weight and the molecular weights of its component ions which were produced from the compound via collisionally induced decomposition (CID).

Mass Spectrogram (mass spec for short)

An analytical device into which chemical compounds are introduced and then ionized. The ions are separated by their mass to charge ratios and then detected by an electron multiplier, which is connected in some manner to a computer. The data produced consists of an array of mass/charge and abundance data points (called a mass spectrum). To further complicate things, a device known as a chromatograph (liquid or gas based) is connected to the sampling inlet of the mass spectrometer. The chromatograph is capable of separating a mixture of chemical compounds prior to introducing them into the mass spectrometer for detection. These combined systems are called chromatograph-mass spectrometers, abbreviated as GC/MS or LC/MS depending on whether they are gas or liquid based separations. (See “Total Ion Chcromatogram,” “Precursor Ion Chromatogram,” “Neutral Loss Chromatogram,” “Base Peak Chromatogram,” “Extracted Ion Chromatogram,” and “Chcromatogram”)

Microarray

mzXML

XML format proposed by a group at the Institute for Systems Biology for exporting raw mass spec data in a common format readable by all software.

Neutral Loss Chromatogram (NLC)

A (mass spec) chromatogram in which the y-axis for each point on the chromatogram represents the intensity of any product ion in the mass spectrum underlying that point in which the mass offset of the product ion from the precursor ion matches the neutral mass offset specified by the user. (See “Mass Spectrogram”)

Precursor Ion Chromatogram (PIC)

A (mass spec) chromatogram in which the y axis for each point on the chromatogram represents the intensity of any precursor ion in the mass spectrum underlying that point in which the precursor ion yielded a product ion with the mass to charge ratio specified by the user. (See “Mass Spectrogram”)

Total Ion Chromatogram (TIC)

The chromatogram produced from an LC/MS experiment which is the sum of all the intensities of the individual ions at each time interval in the experiment. (See “Mass Spectrogram”)

NCBI

(acronym=????) A repository for many (if not all) publicly available BioInformatics related databases (see GenBank)

GenBank

A set of publicly available BioInformatics (genomic and proteomic) related databases. Available at NCBI. (see NCBI)

PDB

The Protein Data Bank. A database of protein secondary and tertiary protein structures

Primary structure

The sequence of amino acids making up a protein. (See secondary structure and tertiary structure)

Secondary structure

The arrangement of primary structure sequences into commonly occurring shapes, such as Beta Helices and Alpha sheets (See primary structure and tertiary structure)

Tertiary structure

The arrangement of all of the atoms in a protein in three dimensions. (See primary structure and secondary structure)

Grid Glossary

MDS

Globus
Metadata Directory Service
an information service. Based on LDAP. Can be used to store/retrieve data

GIIS

Globus
Grid Index Information Service
an information service. Can be used to query information located on several GRIS servsers. Equivalent of "yellow pages." An implementation of MDS.

GRIS

Globus
Grid Resourse Information Service
an information service. Supplies information about a specific resource. Equivalent of "white pages." An implementation of MDS.

LDAP

Industry Standard
ftp://ftp.ietf.org/internet-drafts/draft-wahl-ldapv3-defns-00.txt
Lightweight Directory Access Protocol
an information service. Can be used to store/retrieve data

Distinguished Name

Industry Standard
uniquely names an entity - format seems to be varied and I can't find the location of the format documentation

Globus

A system and software development environment to develop and run distributed systems

NWS

Network Weather Service
A tool that helps determine throughput of specific network connections and helps to make performance predictions.

Pablo

A tool for entering sensors into distributed applications and detecting the overall performance. Synonym: AutoPilot

AutoPilot

A tool for entering sensors into distributed applications and detecting the overall performance. Synonym: Pablo

MPI

Message Passing Interface
a standard of how messages can be passed

MPICH

Message Passing Interface Chamelion
a portable implementation of MPI (Chamelion because it's portable)

MIPCH-G

MPICH Grid Enabled - a version of MPICH that works with Globus

SSLeay

Secure Socket Layer ??
a software package to aid development of software using the internet using secure sockets

OpenLDAP

an implementation of LDAP

gatekeeper

(in Globus) (This might be inaccurate) Daemon that runs on the remote machine and is used to submit jobs to that machine.

ScalAPACK

a distributed application that calculates matrices or something ????

BLACS

Unknown - perhaps Application - from UIUC

ATLAS

Unknown - perhaps Application - from UIUC

RIB

Unkonwn - perhaps has something to do with managing software versions

CACTUS

Pluggable distributed services to aid in building distributed applications

mapfile

(Globus setup file) A file that contains the Distinguished Names of people who can run distributed Globus applications on this machine

GrADS

A tool to compile and deploy distributed applications

GriPhyN

A network to run huge data crunching Physics applications

Condor

http://www.cs.wisc.edu/condor
A generic resource manager. Facilites a personal job queue for submission on the grid.

Globus Jobmanager

A part of the Globus toolkit that is responsible for launching processes on remote machines.

NimrodG

http://www.globus.org/applications/nimrod.html
A tool written in python that facilitates parameter study submissions on the grid. Also, they are working on Computational Economy and Deadline based Grid Resource Brokering (GRB) and Scheduling. More information on this can be found at: http://www.csse.monash.edu.au/~rajkumar/ecogrid/index.html

GRAM

Globus Resource Allocation Manager
A service inside of Globus to manage resources generically

GSI

Globus Security Infrastructure
http://www.globus.org/toolkit/security.html and http://www.globus.org/security/
A service inside of Globus. The Grid Security Infrastructure (GSI) is a set of libraries and tools provided with the Globus Toolkit that enable secure authentication over an open network. The GSI is based on the Generic Security Service API (GSS-API) an IETF standard security API. GSS-API provides a standard API that can be used with a variety of underlying security systems, such as PKI and Kerberos. Thus, Globus can be implemented using PKI (Public Key Infrastructure) or Kerberos. The standard Globus distribution uses a PKI-based security system using Eric A. Young's implementation of SSL, the Secure Sockets Layer.

slapd

An implementation of LDAP

GUSTO

Globus Ubiquitus Supercomputing Testbed
a testbed of machines used previously with Globus

NEXUS

a communication package used in old versions of MPICH and MPICH-G (but not MPICH-G2)

SNMP

Simple Network Management Protocol
Standard Information Service. Not to be confused with SMTP which is an e-mail protocol.

NIS

Network Information Service
A standard information service

GSS

http://www.scit.wlv.ac.uk/rfc/rfc15xx/RFC1508.html and http://www.scit.wlv.ac.uk/rfc/rfc15xxRFC1509.html and http://www.globus.org/security/implementation.html
Generic Security System or Generic Security Service
defines a standard procedure and API for obtaining credentials (passwords or certificates) for mutual authentication (client and server), and for meessage-oriented encryption and decryption.
Perhaps this next sentence should be for GSI instead of GSS?
GSS is independent of any particular security system and can be layered on top of different security methods such as Kerberos and SSL

ch_p4

a "device" that MPICH uses to transmit the message this device is TCP. If you're running MPICH with Globus, the device should probably be Globus

LDIF

LDAP Data Interchange Format.
An LDAP object which means it is data that can be viewed through LDAP (or a GIIS/GRIS).

hbm

Heart Beat Monitor.
Tools for monitoring the status of processes and reporting failures. Sends regular data packets. If these are not received, then the process at the receiving end knows that there is a problem somewhere.

trilabs

The three weapon labs, Los Alamos, Lawrence Livermore and Sandia

HPSS

http://www.sdsc.edu/hpss/hpss1.html
High Performance Storage System.

DRM

http://www.llnl.gov/asci/pse/hpcs/drm/drm.html
The ASCI Distributed Resource Management group.
This appears to be a software tool in use by trilabs (especially at Lawrence Livermore National Labs) to manage their resources.

DUROC

http://www.globus.org/duroc/
The Dynamically-Updated Request Online Coallocator.
A layer on top of GRAM to provide multiple, simultaneous job submission and management(co-allocation).

PBS

Portable Batch System
Used for scheduling jobs on high-end resources, typically- www.openpbs.org. Globus supports most scheduling systems including PBS, LSF, NQE and has an interface to Condor as well.

LoadLeveler

System for scheduling jobs. Globus supports most scheduling systems including PBS, LSF, NQE and has an interface to Condor as well.

LSF

System for scheduling jobs. Globus supports most scheduling systems including PBS, LSF, NQE and has an interface to Condor as well.

XML

http://www.cs.uchicago.edu/~dangulo/soap
A Standardized Generalized Markul Language that allows you to create other markup languages (like HTML, but HTML is not technically XML but SGML which is basically the same thing).

SOAP

http://www.cs.uchicago.edu/~dangulo/soap
An XML based Data Transport Protocol

XKMS

http://www.sunworld.com/sunworldonline/swol-12-2000/swol-1201-verisign.html
An XML based Net Security Protocol

IPsec

Unknown - has something to do with security.

DOM

(Document Object Model) The parsed tree of XML objects.

SAX

XML parser.

Object Class

ftp://ftp.ietf.org/internet-drafts/draft-wahl-ldapv3-defns-00.txt
The term "Object Class" is defined in X.501(1993) section 8.3. In LDAP, there are four kinds of object class: abstract (XREF), structural (XREF), auxiliary (XREF) and the extensible object class (XREF). The extensible object class is not defined in X.500.
The object class governs the attributes in an entry.

RSL

http://www-fp.globus.org/gram/rsl_spec1.html
Resource specification Language. A common interchange language to describe resources. This is used internally (and externally if wished) to start Globus jobs.

GASS

http://www.globus.org/gass/
Global Access to Secondary Storage.
GASS simplifies the porting and running of applications that use file I/O to the Globus environment. Libraries and utilities are provided to eliminate the need to manually login to sites and ftp files or install a distributed file system. The APIs are designed to allow reuse of programs that use Unix or standard C I/O with little or no modification.

HDF5

http://hdf.ncsa.uiuc.edu/HDF5/
Hierarchical Data Format.
At its lowest level, HDF is a physical file format for storing scientific data. At its highest level, HDF is a collection of utilities and applications for manipulating, viewing, and analyzing data in HDF files. Between these levels, HDF is a software library that provides high-level APIs and a low-level data interface.

FQDN

Abbreviation of Fully Qualified Domain Name.
This is required in many instances to uniquely identify a machine on the InterNet. The FQDN must be used in the mapfile and is used in LDAP installation process. FQDNs are in the form <hostname>.<domainname> Example: eros.airius.com

Vampir

http://www.ncsa.uiuc.edu/Apps/Math/Vampir/
A graphical tool for displaying the compute time and the communication latency time for distributed applications. A URL that shows off its power is href="http://www.ncsa.uiuc.edu/Apps/Math/Vampir/global_displays.htm

NCSA

http://www.ncsa.uiuc.edu/
National Center for Supercomputing Applications.
A research facility for Supercomputing at UIUC.

GuideView

http://www.kai.com/parallel/kappro/guideview/
GuideView is a tool from NCSA and KAI. It is an X Window based performance data browser, designed to make it easy to identify and eliminate parallel performance bottlenecks.

KAY

http://www.kai.com/
A division of Intel associated with UIUC and NCSA.

OpenMP

http://www.openmp.org/
The OpenMP Application Program Interface (API) supports multi-platform shared-memory parallel programming in C/C++ and Fortran on all architectures, including Unix platforms and Windows NT platforms. Jointly defined by a group of major computer hardware and software vendors, OpenMP is a portable, scalable model that gives shared-memory parallel programmers a simple and flexible interface for developing parallel applications for platforms ranging from the desktop to the supercomputer.

NUMA

http://www.ncsa.uiuc.edu/SCD/Training/materials/html/intro/tsld050.htm
Non-Uniform Memory Access.
This attribute of machines must be considered when programming in a distributed environment. A large component contributing to this non-uniformity is data locality.

PVM

http://www.ncsa.uiuc.edu/SCD/Hardware/CommonDoc/MessPass/
Parallel Virtual Machine.
A message passing standard in competition with MPI.

HPF

http://www.ncsa.uiuc.edu/SCD/Hardware/CommonDoc/HPF.html
High Performance Fortran.

Fortran 90

http://www.nsc.liu.se/f77to90.html

SMP

http://scv.bu.edu/SCV/Tutorials/SMP/intro.html
Symmetric Multiprocessing.
SMP refers to the architecture used in some multiple processor computers, including the SGI machines. In some architectures, one or more processors may have capabilities not available to the remaining processors. SMP is an egalitarian arrangement in which all processors have full and equal functionality. The term SMP is often used synonymously with "shared memory".

DMP

http://www.serc.iisc.ernet.in/facilities/software/hpc.html
Disrtibuted Memory Programming.
Achitectures of distributed computing where the processors' memory is not shared (see SMP).

AWI

http://www.ncsa.uiuc.edu/VMR/UserGuides/AWI.html
Alliance Wide Interface.
Provides a common interface between the various mass storage systems and archival methods found in the Alliance.

Alliance

http://www.ncsa.uiuc.edu/SCD/Alliance/
National Computational Science Alliance.
This is part of NCSA but not another meaning for the NCSA acronym. The Alliance offers allocations on high-performance and high-throughput systems around the county to advance computational science and to help develop systems and applications that will be part of the National Computational Grid.

GMA

http://www-didc.lbl.gov/GridPerf/ and http://www-didc.lbl.gov/GridPerf/papers/GMA.pdf
Grid Monitoring Architecture.
By the Grid Performance Working Group. There are several research groups that are developing Grid Monitoring Systems to monitor and manage distributed computing components. This is critical to determine the source of performance problems, to tune the system and application for better performance, to determins if a server is down, and to determine whether to restart a server and to determine whether to redirect service requests elsewhere. GMA is targeted at helping these groups and their systems interoperate. $ Grid Performance Working Group
http://www-didc.lbl.gov/GridPerf/
A Working Group focused on defining standards and best practices for the gathering, representation, storage, distribution, and query of performance information about Grid resources and applications. A Working Group in the Global Grid Forum.

Global Grid Forum

http://www.gridforum.org/
The Global Grid Forum (Global GF) is a community-initiated forum of individual researchers and practitioners working on distributed computing, or "grid" technologies. Global GF is the result of a merger of the Grid Forum, the eGrid European Grid Forum, and the Grid community in Asia-Pacific.
Global GF focuses on the promotion and development of Grid technologies and applications via the development and documentation of "best practices," implementation guidelines, and standards with an emphasis on rough consensus and running code.

OSCAR

http://www.csm.ornl.gov/oscar/
Open Source Cluster Application Resource.
By the Open Cluster Group. A cluster-in-a-box package developed to lower the entry barriers into the cluster computing world and to eliminate the need for a cluster expert. OSCAR provides a single CD with a wizard-driven interface to building a cluster. It is designed to provide the most popular and universal cluster software available in open source. At the end of the wizard process, the cluster will be ready to run MPI or PVM jobs using the Portable Batch System (PBS). C3 tools are included for management and ssh for secure transactions.

Open Cluster Group

http://www.OpenClusterGroup.org
The Open Cluster Group is an informal consortium of commercial and research organizations involved with cluster-computing. Their mission is to make clusters a realistic option for organizations that use high performance computing to accomplish their goals.

GiB

Grid in a Box.
A shrink-wrapped version of Globus based software to allow easy Grid setup. Created by collaboration of Globus (DSL at Argonne) and NCSA folks.

Grid in a Box

See GiB.

PKI

A Cryptographic standard based on Public and Private Keys

SSL

Secure Sockets Layer.
A cryptographic standard to use sockets securly. Based on PKI.

GSI

http://www.globus.org (better link needed)
A Cryptographic standard from Globus based on PKI. It adds Proxy credentials, delegation, and restricted delegation to the PKI standard.

PSE

http://www-cgi.cs.purdue.edu/cgi-bin/acc/pses.cgi
http://vtopus.cs.vt.edu/~pse/intro.html
Problem Solving Environment.
An advanced aid to users that enables them to use computers using the vocabulary of their domain and with little knowledge of the computers themselves.

Other Grid Glossaries

• [[http://www.hku.hk/cc/sp2/workshop/html/glossary/glossary.html][Maui High Performance Computing Center Glossary}}
• Globus Security Glossary
• GIS Terms Glossary

-- DaveAngulo - 20 Oct 2005