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In an appeal posted on its Web site this week, the group warned that the DoD should "avoid crafting needless and potentially detrimental IT policy to promote the use" of open-source software.
Open source generally refers to any software program whose source code is made freely available to other developers and users for use and development without restrictions.
The ISC includes Microsoft, Cisco and Intel as members and is chaired by a group known for its close ties to Microsoft, the Computing Technology Industry Association, or CompTIA.
The appeal by the ISC was made in response to a report released on 6 November by defence contractor Mitre, Use of free and open sources software in the US Department of Defense.
The report endorsed free and open software as an alternative to proprietary software, saying that it "plays a more critical role in the [Defense Department] than has been generally recognised".
The ISC countered that "the DoD should not openly promote" the use of open software because it may not be, in all cases, the software best suited for a project. Furthermore, the DoD should also "not be fettered by a preconception that open source software is somehow inherently more secure," the ISC said.
In October, CompTIA and the ISC were accused by open source advocates, including former Hewlett-Packard employee Bruce Perens, of attempting to lock open-source software out of the government marketplace while posing as a group promoting fairness in governmental software procurement.
CompTIA has denied such accusations, stressing that it is simply promoting the idea that governments should buy software that best meets their needs. Despite garnering support from Microsoft and Intel, the group has asserted it is not fronting or acting as a mouthpiece for Microsoft.
In its appeal to the DoD, the ISC also took issue with the General Public Licence (GPL), which lets developers view and modify the source code of GPL software as long as any modifications made are freely available to other users.
"While the law on this matter remains untested, it makes sense for companies to be highly risk-averse in this area, striking a more defensive posture when confronted with software development that may implicate GPL code or similar coding environments. Commercial and hybrid software developers generally do not want to risk losing their investment," the ISC said.
As governments look to open-source software as a cheaper and possibly more secure alternative to proprietary software, software companies such as Microsoft have become more organised in opposing its use.
This year Linux made inroads among European government agencies in Germany, France and Finland when they chose open-source software for various purposes.
Additionally, some agencies in the UK are looking to adopt open source because of a dislike for Microsoft's End-User Licensing Agreements (EULAs). In some cases, Microsoft has been forced to concede to lower licensing agreement fees.