I keep seeing this intense focus on one specific technology in each advocacy group within the 'green' movements. Such as ethanol, biodiesel, wind even algae. I do not think any of these BY THEMSELVES can accomplish anything except causing more problems for society as a whole. The environmental impact of each individual technology by itself is devastating to society in the long term. No One seems to want to recognize the environmental impacts of their favorite green project, for example the devastation to the bird populations around the windmill farms. ALL green technologies need to be pursued in NATURAL combinations with complementary natural systems if we are going to have long term benefits without devastating 'side effects'.
EXAMPLE I raise tilapia and vegetables in an integrated system of aquaponics. I produce a balanced food supply. The system also produces algae, fish food supplements and livestock feeds.
SO, upstream / downstream I don't think are anywhere nearly as important as integration with other systems that both benefit from and provide benefits to the primary product.

Downstream can’t be a neglected aspect in algae biodiesl production. Extraction and conversion to energy products are expensive today and hence do present some challenges. It is also a fact that algae oil could present some difficulties in transesterification owing to its high free fatty acids (FFA) content.

The upstream processes for algae oil comprise steps quite unique to this industry. Some of these processes, for instance algal strain selection or cultivation needs a different approach than the traditiional methods that we have been using over ceturies for plants. The downstream operations for algal oil, which comprise extraction and conversion of the harvested algae into final fuel products, in contrast, are relatively well understood technologies currently practiced on a large scale and the same facilities can be adapted or modified to produce biodiesel from algae.

As far as strain and cultivation is concerned we have much more. As on today the technology experts should focus on development of economical options for harvesting. If harvesting makes its way, this sector will helps community in many ways, not only the energy substitute or the neutraceutical supplement.