I wrote a short paper recently regarding a web application I developed, but had a hard time in finding a list of journals which would publish short tool and software, web-application, database articles except Bioinformatics Applications Note (2-3 pages).
I would like to create a resource for that here at Biostars, and would list the ones I know. Please add more as an answer, I will accept all of them, if they are satisfy the criteria (2-3 pages, software/app/database submission + Bioinformatics)
Application Notes (up to 2 pages; this is approx. 1300 words or 1000 words plus one figure) Applications Notes are short descriptions of novel software or new algorithm implementations, databases and network services (web servers, and interfaces). Software or data must be freely available to non-commercial users. Availability and Implementation must be clearly stated in the article. Authors must also ensure that the software is available for a full TWO YEARS following publication. Web services must not require mandatory registration by the user. Additional Supplementary data can be published online-only by the journal. This supplementary material should be referred to in the abstract of the Application Note. If describing software, the software should run under nearly all conditions on a wide range of machines. Web servers should not be browser specific. Application Notes must not describe trivial utilities, nor involve significant investment of time for the user to install. The name of the application should be included in the title.
(iv) Technical briefs describing the development of a novel method or an improvement or noteworthy modification of an already existing technique or platform used in proteomic analysis. These manuscripts should bear the words "Technical Brief" immediately above the title on the first page. They should not be subdivided into titled sections but written in a continuous style. Technical briefs should not exceed 2500 words (including references as well as figure and table legends) and contain no more than three display elements (figures and tables).
(v) Dataset briefs describing novel proteomic data sets of specific types of samples, such as organisms, tissues, cells, microbes, viruses and organelles. These data sets can be generated with any proteomic platform including two-dimensional gels, mass spectrometry or protein arrays. An important criterion is that the data set contains a significant number of identified proteins that will benefit further research on that particular sample type. Biological replicates are needed and their number must be detailed in the text. Purely descriptive manuscripts (e.g. cataloguing the proteome of a single sample type) will only be considered as Dataset briefs. The manuscripts should bear the words "Dataset Brief" immediately above the title on the first page. They should not be subdivided into titled sections but written in a continuous style. Data set briefs should not exceed 2500 words (including references as well as figure and table legends) and contain no more than three display elements (figures and tables). Authors are encouraged to submit supporting information, such as annotated two-dimensional gel images and tables of protein identifications, which will only appear online. Deposition of supporting data in a public and global open access database is mandatory (see Section 5.6). Examples of such suitable global, open access databases are the ProteomeXchange consortium (http://www.proteomexchange.org) (including receiving repositories PRIDE and PASSEL) or World-2DPAGE (http://world-2dpage.expasy.org/repository/).
Applications Note (Example)
4) Biorxiv - A pre-print server geared towards Biology