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History of RDP


University of Illinois at Urbana-Champaign Period


The RDP arose out of research conducted by two University of Illinois at Urbana-Champaign (UIUC) faculty members, Carl R. Woese and Gary J. Olsen. Woese recognized that, due to rRNA's conserved sequence, ribosomal RNA could be used to elicit phylogenetic relationships between organisms. They foresaw that making a collection of rRNA sequences available would be useful to the research community and stimulate research in this area. Initial funding for the RDP was awarded in 1989 by the Biological Instrumentation and Resources Program of the National Science Foundation. Argonne National Laboratory first hosted the RDP ftp and public sites and on January 5, 1992, 471 16S rRNA sequences, many of which were generated in Woese's laboratory, were made available to the public in the first release of the RDP. The public sites were moved to UIUC for Release 3.0 in August 1993. NSF predominantly supported the RDP to 1997. As data were originally stored as flat files, additional funding to migrate to a commercial database management system was awarded jointly to Michigan State University (MSU) and UIUC in 1995. During the last 18 months of core NSF funding, discussions with MSU faculty at the Center for Microbial Ecology led to the relocation of the RDP to MSU.


Michigan State University Period


With dbms migration and collaboration between MSU and UIUC begun, official support of the RDP by the Center for Microbial Ecology at MSU started December 1997. The RDP Curator continued to physically work at UIUC but participated in planning meetings for the RDP's official move to MSU in 1998. The first data release and official announcement of the RDP-II WWW site occurred on July 31, 1998.

For Relases 7.1 and 8.0, RDP-II staff members at MSU included Bonnie Maidak, responsible for curation and user support, and Jim Cole, who oversaw, and continues to oversee, the website, database and development. Other staff members (Tim Lilburn, Chuck Parker, and Paul Saxman) served as curatorial assistants, system administrators, and programmers. Bonnie and Chuck left the RDP-II before Release 8.1 appeared, although they contributed substantially to the Release.

Release 9.0 marked a substantial change to the RDP. Due to an explosion of sequence data being made available by sequence repositories, RDP's previous methods and programs needed substantial refactoring to bring them into the modern era. Hand alignments were replaced by an auto-aligner, allowing faster and more consistent database updates. Analyses tools needed to be rewritten to handle the hugely increased number of sequences, and interfaces improved to match modern standards. Perhaps most importantly, the concept of an infrequent, monolithic release was also replaced with the idea of highly automated monthly incremental updates. These updates allow the RDP to maintain up-to-date data and deploy new tools between releases.

Two MSU faculty members from the Departments of Microbiology (Jim Tiedje and George Garrity) serve in an advisory role. The RDP-II is currently funded by the Office of Biological and Environmental Research of the US Department of Energy (OBER-DOE), the National Science Foundation (NSF), the National Institutes of Health (NIH), and the State of Michigan.

Complete web statistics on this public server are available. During the first year of operation, the new website served over 15,000 distinct hosts from over 40 countries and averaged over 26 M bytes of data transferred per day. In order to determine the needs and perceptions of its user community, in early 1999 the RDP-II solicited user comments via a user survey. Most users felt that RDP-II should devote more resources to prokaryotic small subunit sequences, and that RDP-II could improve by releasing data in a more timely manner.

Since the first published article describing the RDP in 1991 (Olsen et al., 1991a), eight additional articles describing the RDP have been published in the annual databases issue of Nucleic Acids Research. These nine articles have been cited 2,087 times in journals covering areas of research such as AIDS, bioinformatics, dairy science, environmental microbiology, fermentation bioengineering, gastroenterology, and veterinary medicine, to name just a few.


RDP Release Dates and Info:


Release
Number

Date

Sequence Type and Number

Small Subunit
(SSU)

Large Subunit
(LSU)

Current
11.4

Alignment model updated to training set No. 14,
hand-curated Warcup Fungal ITS training set and
Monthly updates beginning
May 2015

3,224,600 16S
108,901 Fungal 28S
n/a
11.x New alignment, Fungal data and
Monthly updates beginning
October 2013
2,809,406 16S
62,860 Fungal 28S
n/a
10.x New alignment and
Monthly updates began
May 2008
550,366 Prokaryotic n/a
9.x New alignment and
Monthly updates began
September 2001
>100,000 Prokaryotic n/a
8.1 21 May 2001 16277 Prokaryotic 72 All
5201 Eukaryotic
1503 Mitochondrial
34531 Unaligned 1400 Unaligned
8.0 1 Jun 2000 16277 Prokaryotic 72 All
2055 Eukaryotic
1503 Mitochondrial
30322 Unaligned 1400 Unaligned
7.1 17 September 1999 7322  Prokaryotic 72 All
2055  Eukaryotic
1503  Mitochondrial
21476  Unaligned 1400 Unaligned
7.0  31 July 1998 6205  Prokaryotic 72 All
2055  Eukaryotic
1503  Mitochondrial
22326  Unaligned 1400 Unaligned
6.1  27 June 1997 4332  Prokaryotic 72 All
437  Eukaryotic
1066  Mitochondrial
10744  Unaligned 1400 Unaligned
6.0  15 June 1997 4332  Prokaryotic 72 All
437  Eukaryotic
1066  Mitochondrial
10744  Unaligned 1400 Unaligned
5.0 17 May 1995 2849  Prokaryotic 72 All
437  Eukaryotic
5505  Unaligned 1400 Unaligned
4.1  24 October 1994 2251  Prokaryotic 72 All
437  Eukaryotic
4456  Unaligned 891 Unaligned
4.0 18 Jun 1994 2251  Prokaryotic 72 All
437  Eukaryotic
3.1  24 October 1993 1379  Prokaryotic 72 All
236  Eukaryotic
3.0 1 August 1993 1379  Prokaryotic 72 All
236  Eukaryotic
2.1 5 March 1993 651  Prokaryotic 72 All
236  Eukaryotic
2.0  15 February 1993 651  Prokaryotic 72 All
236  Eukaryotic
1.0 5 January 1992 471  Prokaryotic 72 All
165  Eukaryotic

 

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