Spinneret is a structured storage engine that can be thought of as an extended tuple storage system. It takes the best aspects of relational, object, and hierarchical databases and throws away the dead weight associated with those technologies. The benefit of Spinneret is that its data model is incredibly flexible, allowing it to expose its underlying data in any number of ways. It operates similar to an object database, but without hard ties to an originating language, and can also behave like a relational database without the burden of complex joins.
ProteomeCommons.org IO Framework is a proper Java framework for handling spectra and peak lists. The framework can read and write to a number of different spectra and peak list formats, and it provides a simple, intuitive Java object model for working with spectra or peak lists. All classes support two methods of handling peak list and spectrum data: in-memory or stream. The goal of this framework is to support all the popular MS and MSMS data formats, and to eliminate any time or effort involved in figuring out how to read and write peak list or spectrum files.
ProteomeCommons.org Java Analysis Framework is a framework for referencing common mass spectrometry data such as atoms and residues. This framework provides a programmer with an easy-to-use library for writing programs that rely on common mass spectrometry data. The framework also contains utilities such as an isotope calculator and a reference for residue abbreviations.
jrawio is a Service Provider Implementation for the Java Image I/O API that provides the capability to read images stored in a "camera raw" format. It supports various formats from the major camera manufacturers (e.g. NEF, CRW, CR2, PEF, SRF, MRW) as well as Adobe Digital Negative Format (DNG). It is made of pure Java code and does not require any native library.
CTL is a cross-platform control dispatching tool that makes it easy to automate any kind of distributed systems management or application provisioning task. Rather than writing complex and error-prone scripts that over utilize "for loops", CTL handles the network dispatching for you and allows you to focus on the actual management tasks you need to accomplish. In addition to being a dispatching tool, CTL comes with pre-built cross-platform utilities so you don't have to script actions like file distribution or process and port checking. You can also write your own custom utilities and share them with others in your organization. Custom utilities are defined in XML, and your scripting can be done in multiple scripting languages (Perl, Python, etc.), *nix shell, Windows batch, and/or Ant.
jniThreadCPUUsage is a Java library to get the amount of user and system CPU time used per thread. This is done via JNI, which calls getrusage() on the system. getrusage() is only available on Linux 2.6.26 or later and Solaris. One useful application of this is measuring the amount of CPU time used for a servlet request. getrusage() CPU time reporting is better than using the real time clock because it measures actual CPU time used and disregards times when the thread is idle or waiting (such as when it is waiting for network I/O).
junixsocket is a Java/JNI library that allows the use of Unix Domain Sockets (AF_UNIX sockets) from Java. In contrast to other implementations, junixsocket extends the Java Sockets API (java.net.Socket, java.net.SocketAddress, etc.) and even supports RMI over AF_UNIX. It is also possible to use it in conjunction with Connector/J to connect to a local MySQL server via Unix domain sockets.
Ametys is a powerful Web CMS used by many institutions of higher education and government, but also industries and SMEs. It is known for its ergonomic design which promotes ease of use, its social Web functionality, and the ability to manage a large number of users. It makes content publishing accessible for the non-programmer and provides an easy editorial interface very similar to Microsoft Office applications.